Biotechnology Commons^™

Crystal Structures And Kinetics Of Monofunctional Proline Dehydrogenase Provide Insight Into Substrate Recognition And Conformational Changes Associated With Flavin Reduction And Product Release, Min Luo, Benjamin W. Arentson, Dhiraj Srivastava, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline dehydrogenase catalyzes the FAD-dependent oxidation of proline to Δ1- pyrroline-5- carboxylate, which is the first step of proline catabolism. Here, we report the structures of proline dehydrogenase from Deinococcus radiodurans in the oxidized state complexed with the proline analog L-tetrahydrofuroic acid and in the reduced state with the proline site vacant. The analog binds against the si face of the FAD isoalloxazine and is protected from bulk solvent by the α8 helix and the β1-α1 loop. The FAD ribityl chain adopts two conformations in the E-S complex, which is unprecedented for flavoenzymes. One of the conformations is novel for …

Doublesex Target Genes In The Red Flour Beetle, Tribolium Castaneum, Jayendra Nath Shukla, Subba Reddy Palli

Entomology Faculty Publications

Sex determination cascade in insects terminates with the production of sex-specific protein, Doublesex (Dsx). We identified the dsx homolog (Tcdsx) in Tribolium castaneum. The pre-mRNA of Tcdsx is sex-specifically spliced into three female (Tcdsxf1, Tcdsxf2 and Tcdsxf3) and one male-specific (Tcdsxm) isoforms. Cis-regulatory elements potentially involved in sex-specific splicing of the Tcdsx pre-mRNA were identified in the female-specific exon and the adjoining intronic sequences. All the three female-specific TcDsx proteins share common OD1 and OD2 domains and differ in their C-terminal sequences. Knockdown of Tcdsx resulted in a reduction in the oocyte development, egg production and hatching of eggs laid. …

Knockout Of The 15 Kda Selenoprotein Protects Against Chemically-Induced Aberrant Crypt Formation In Mice, Petra A. Tsuji, Bradley A. Carlson, Salvador Naranjo-Suarez, Min-Hyuk Yoo, Xue-Ming Xu, Dmitri E. Fomenko, Vadim Gladyshev, Dolph L. Hatfield, Cindy D. Davis

Department of Biochemistry: Faculty Publications

Evidence suggests that selenium has cancer preventive properties that are largely mediated through selenoproteins. Our previous observations demonstrated that targeted down-regulation of the 15 kDa selenoprotein (Sep15) in murine colon cancer cells resulted in the reversal of the cancer phenotype. The present study investigated the effect of Sep15 knockout in mice using a chemically-induced colon cancer model. Homozygous Sep15 knockout mice, and wild type littermate controls were given four weekly subcutaneous injections of azoxymethane (10 mg/kg). Sep15 knockout mice developed significantly (pGBP-1 in humans has been associated with a highly significant, increased five-year survival rate in colorectal cancer patients. In …

Role Of Polymeric Excipients On Controlled Release Profile Of Glipizide From Plga And Eudragit Rs 100 Nanoparticles, Pratap Naha, Hugh Byrne, Amulya Panda

Articles

Polylactic-co-glycolic acid (PLGA) 50:50 and Eudragit RS 100 nanoparticles entrapping glipizide along with excipients were prepared using single emulsion solvent evaporation method. The objective was to develop single oral dose glipizide nano particles for reducing blood sugar level in diabetes induced experimental animals. Incorporation of Polyethylene glycol (PEG) (0.5%), Hydroxypropyl methylcellulose (HPMC) (0.5%) and Tween 20 (0.5%) in the organic phase during particle formulation improved release profile of glipizide from the polymer particles. Entrapment efficiency of glipizide in all the polymeric formulations was around ~70 %. Around 80 % of glipizide was released from both PLGA and Eudragit …

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 …}

Scribble Acts In The Drosophila Fat-Hippo Pathway To Regulate Warts Activity, Shilpi Verghese, Indrayani Waghmare, Hailey Kwon, Katelin Hanes, Madhuri Kango-Singh

Biology Faculty Publications

Epithelial cells are the major cell-type for all organs in multicellular organisms. In order to achieve correct organ size, epithelial tissues need mechanisms that limit their proliferation, and protect tissues from damage caused by defective epithelial cells. Recently, the Hippo signaling pathway has emerged as a major mechanism that orchestrates epithelial development. Hippo signaling is required for cells to stop proliferation as in the absence of Hippo signaling tissues continue to proliferate and produce overgrown organs or tumors. Studies in Drosophila have led the way in providing a framework for how Hippo alters the pattern of gene transcription in target …

Cross Regulation Of Sirtuin 1, Ampk, And Ppary In Conjugated Linoleic Acid Treated Adipocytes, Shan Jiang, Wei Wang, Jess Miner, Michael E. Fromm

Department of Biochemistry: Faculty Publications

Trans-10, cis-12 conjugated linoleic acid (t10c12 CLA) reduces triglyceride (TG) levels in adipocytes through multiple pathways, with AMP-activated protein kinase (AMPK) generally facilitating, and peroxisome proliferator-activated receptor γ (PPARγ) generally opposing these reductions. Sirtuin 1 (SIRT1), a histone/protein deacetylase that affects energy homeostasis, often functions coordinately with AMPK, and is capable of binding to PPARγ, thereby inhibiting its activity. This study investigated the role of SIRT1 in the response of 3T3-L1 adipocytes to t10c12 CLA by testing the following hypotheses: 1) SIRT1 is functionally required for robust TG reduction; and 2) SIRT1, …

Form And Function Of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon Wolfaardt, Grant Allen, Steven N. Liss, Lee R. Lynd

Dartmouth Scholarship

The importance of bacterial adherence has been acknowledged in microbial lignocellulose conversion studies; however, few reports have described the function and structure of biofilms supported by cellulosic substrates. We investigated the organization, dynamic formation, and carbon flow associated with biofilms of the obligately anaerobic cellulolytic bacterium Clostridium thermocellum 27405. Using noninvasive, in situ fluorescence imaging, we showed biofilms capable of near complete substrate conversion with a characteristic monolayered cell structure without an extracellular polymeric matrix typically seen in biofilms. Cell division at the interface and terminal endospores appeared throughout all stages of biofilm growth. Using continuous-flow reactors with a rate …

Naturally Selecting Solutions: The Use Of Genetic Algorithms In Bioinformatics, Timmy Manning, Roy D. Sleator, Paul Walsh

Department of Biological Sciences Publications

For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the …

Setting The Sound Up For Success, Hillary Kenyon

Wrack Lines

Deploying remotely-set disease-resistant oyster seed in biodegradable netting on a natural bed in Connecticut. The eastern oyster, Crassostrea virginica, is a keystone species in Connecticut's coastal environment.

Sex Determination In Beetles: Production Of All Male Progeny By Parental Rnai Knockdown Of Transformer, Jayendra Nath Shukla, Subba Reddy Palli

Entomology Faculty Publications

Sex in insects is determined by a cascade of regulators ultimately controlling sex-specific splicing of a transcription factor, Doublesex (Dsx). We recently identified homolog of dsx in the red flour beetle, Tribolium castaneum (Tcdsx). Here, we report on the identification and characterization of a regulator of Tcdsx splicing in T. castaneum. Two male-specific and one female-specific isoforms of T. castaneum transformer (Tctra) were identified. RNA interference-aided knockdown of Tctra in pupa or adults caused a change in sex from females to males by diverting the splicing of Tcdsx pre-mRNA to male-specific isoform. All the pupa and adults developed from Tctra …

Improving The Efficiency Of Homologous Gene Replacement By Disrupting Non-Homologous End Joining Pathway Gene Kusa In The Oleaginous Fungus Mortierella Alpina, Kathleen T. Krueger, Ziyu Dai Dr, Ugur Uzuner, Scott E. Baker Dr

STAR Program Research Presentations

Mortierella alpina , a oleaginous filamentous fungus, is one of industrial fungal strains known for the production of arachidonic acid. It is also of particular interest for hydrocarbon biofuel production since it is able to produce up to 50% of its mass in rich, long-chain polyunsaturated fatty acids [PUFA’s]. In addition to high fatty acid production, M. alpina like many other oleaginous fungi, already have mechanisms for accumulating significant concentrations of hydrophobic compounds making it a naturally equipped candidate to handle potential toxic concentrations of hydrocarbons. To date, three different transformation methods have been established for M. alpina that are …

Quantification And In Vitro Analysis Of Nanolipoproteins (Nlps) Containing Adjuvants, Purna Venkataraman, Craig Blanchette, Nicholas O. Fischer

STAR Program Research Presentations

Nanolipoprotein particles (NLPs) self-assemble into nanoscale structures that can be used as vaccines or drug delivery agents. Due to the nature of the NLPs, a variety of immune stimulating compounds or adjuvants can be readily incorporated into NLPs: a characteristic difficult to engineer into most other nanoscale platforms. In light of this, a method for quantifying the amount adjuvant actually incorporated into NLPs is a question of high importance. Through the use of reverse phase High-Performance Liquid Chromatography (HPLC) and an Evaporative Light Scattering Detector (ELSD), standard curves can be constructed by analyzing mixtures of NLP components of known concentration, …

Analyzing Environmental Microbes For Genomic Regions Promoting Ionic Liquid Tolerance In E. Coli, Ann Nguyen, Alison Richins, Thomas Rüegg, Steven Singer, Michael Thelen

STAR Program Research Presentations

Ionic liquids (ILs) are promising as solvents to increase the efficiency of biofuel production; however, ILs are toxic to microbes used in the fermentation of liquid fuels. To engineer IL resistant biofuel hosts, environmental bacteria were screened for tolerance, and these were used to create gene libraries to test in E. coli. Future characterization of these libraries using molecular techniques will be used to identify genes that contribute IL-tolerance to transformed microbes.

Diffusion Barriers Of The Lateral Ventricular System, Anitha Saravanakumar

Master's Theses

Adult neurogenesis in mammalian brain has become a well-accepted phenomenon. The neural stem cells in the sub ventricular zone (SVZ) along the lateral wall of the lateral ventricle, the largest germinal center of adult neurogenesis, are maintained by the neural stem cell niche. One prominent feature of the niche is its close proximity to the cerebral spinal fluid (CSF). The role of micromolecules (such as ions, water and gases) present in the CSF and diffusing through the lateral ventricular wall and how the stem cell micro-environment is maintained is poorly understood. The cytoarchitecture of the lateral ventricular wall with a …

Efficacy Comparison Of Various Pcr Master Mixes And Thermal Cycling Parameters For Detection Of Brucella Abortus In Multiplex Assays, Kevin J. Testo, Jason A. Olivas, Alda C. Carrillo, Pejman Naraghi-Arani

STAR Program Research Presentations

Diagnostic testing for bioterrorism agents in food is essential for the safety and welfare of the general populace. Multiplex assays provide the means to test for multiple pathogen signatures with a single polymerase chain reaction (PCR) test. PCR, Luminex xMAP ® infrared fluorophore bead technology, and flow cytometry, multiplex diagnostic assays are incredibly specific and sensitive to highly conserved regions at various loci in a microbe’s genome. In order to increase the effectiveness of the PCR and the resulting fluorescent response of the beads, different PCR master mix commercial kits were compared to the standard AgPath RT-PCR mix. This study …

Design And Construction Of Automized Assembly Application, Htwe E.E, Hatanaka S, Akiyama T

ASEAN Journal on Science and Technology for Development

Nowadays the main stream of current automatic process and assembly is on intermittent transportation. Robot control systems can be divided into motion control and force control depending on the work. Assembly work is necessary to consider the state of force applied by detection of the force or moment on the fingers of the gripper. In this project, four groups designed and developed each one of the stages of the workpieces until the final piece was delivered; it was composed of three different workpieces. The mechanism was designed to set the shaft and fasten the screw into a vacancy in a …

Implementation Of A Communication Satellite Orbit Controller Design Using State Space Techniques, Hla M.T, Lae Y.M, Kyaw S.L, Zaw M.N

ASEAN Journal on Science and Technology for Development

This research is of great importance for controlling the altitude of a satellite, especially one used for global communications in a geo-stationary orbit. The objective of this research was to advance a design based on the modelling of an orbit controller for a satellite orbiting into a circular orbit. This encompasses a good understanding of the system’s dynamics. Once a satellite is launchedinto a desired orbit, it never remains in this ideal orbit. The external forces present in space cause perturbations to the ideal orbit. To bring the satellite back into the desired orbit, on-board thrusters provide the in-orbit propulsion. …

Ferromagnetic Order In The Intermetallic Alloys Lani5-Xmgx, Ba D.N, Tai L.T, Trung N.T, Huy N.T

ASEAN Journal on Science and Technology for Development

The influences of the substitution of Ni with Mg on crystallographic and magnetic properties of the intermetallic alloys LaNi5-xMgx (x ≤ 0.4) were investigated. The X-ray diffraction patterns showed that all samples were of single phase, and the lattice parameters, a and c, decreased slightly upon chemical doping. LaNi5 is well known as an exchange-enhanced Pauli paramagnet. Interestingly, in LaNi5-xMgx, the ferromagnetic order existed even with a small amount of dopants; the Curie temperature reached the value of room temperature for x = 0.2, and enhanced with increasing x.

Bond Strength Of Glued-In Rods In Malaysian Tropical Timber As Influenced By Adhesive, Diameter And Glueline Thickness, Za'ba N.E.L, Ahmad Z, Ibrahim A

ASEAN Journal on Science and Technology for Development

Failure in wood structure is mainly caused by improper connection design, construction (fabrication) details, or serviceability. Besides using traditional bolting methods such as nails, screws and bolts to join members, timber members also can be connected by using bonded-in joints. However, current knowledge in the use of this type of timber connection is still limited. This study investigated the performance of bonded-in pultruded rods in timber as connections by exploring the effect of a few parameters such as rod type, diameter of the rod, adhesive type and thickness of the glueline. Pull-out tests were used to characterize the strength of …

Nanoherbals In Human Healthcare: A Proposed Research And Development Roadmap I, Ahmad S, Hashim U

ASEAN Journal on Science and Technology for Development

Bioactive secondary metabolites derived from herbs are examined for their suitability of conversion into nanoforms having flexible morphological controls, surface stabilizations and surface functionalization. This can lead to stable chemical conjugations based on molecular recognition for their possible applications in the form of smart pharmaceuticals, nutraceuticals, cosmaceuticals and many other related areas of human healthcare using green chemistry routes. Using the principles of nanoscience and technology in association with genomics and proteomics, an attempt has been made to decipher whether a suitable form of drug discovery and targeted drug delivery like schemes arefeasible in case of such nano phytochemicals using …

Nanoherbals In Human Healthcare: A Proposed Research And Development Roadmap Ii, Ahmad S, Hashim U

ASEAN Journal on Science and Technology for Development

Bioactive secondary metabolites derived from herbs are examined for their suitability of conversion into nanoforms having flexible morphological controls, surface stabilizations and surface functionalization. This can lead to stable chemical conjugations based on molecular recognition for their possible applications in the form of smart pharmaceuticals, nutraceuticals, cosmaceuticals and many other related areas of human healthcare using green chemistry routes. Using the principles of nanoscience and technology in association with genomics and proteomics, an attempt has been made to decipher whether a suitable form of drug discovery and targeted drug delivery like schemes are feasible in case of such nano phytochemicals …

Performance Evaluation Of A Uasb Reactor Using Dairy Wastes, A Ali, S Khan, K.A. Khan

ASEAN Journal on Science and Technology for Development

A UASB reactor of 6-litre capacity, made of acryl material, was operated continuously for 20–22 weeks in three different phases, using actual dairy mill effluent at a constant mesophilic temperature and neutral pH. The dairy wastewater was highly alkaline, turbid and milky in colour with a bad odour. The average COD and BOD concentrations of the dairy mill effluent were observed to be 2945 mg/l and 1070 mg/l, respectively. Phase I was the start-up phase, with OLR of 0.13 g COD/l.d. SLR, effluent VFAs, effluent TSS, biogas production and methane composition observed during this phase were 1.4 g COD/g VSS.d, …

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 …