Biotechnology Commons^™

Design Of A Factorial Experiment With Randomization Restrictions To Assess Medical Device Performance On Vascular Tissue, Wiebke Diestelkamp, Carissa M. Krane, Margaret Pinnell

Biology Faculty Publications

Background: Energy-based surgical scalpels are designed to efficiently transect and seal blood vessels using thermal energy to promote protein denaturation and coagulation. Assessment and design improvement of ultrasonic scalpel performance relies on both in vivo and ex vivo testing. The objective of this work was to design and implement a robust, experimental test matrix with randomization restrictions and predictive statistical power, which allowed for identification of those experimental variables that may affect the quality of the seal obtained ex vivo.

Methods: The design of the experiment included three factors: temperature (two levels); the type of solution used to perfuse the …

Endo-Porter–Mediated Delivery Of Phosphorodiamidate Morpholino Oligos (Pmos) In Erythrocyte Suspension Cultures From Cope's Gray Treefrog Hyla Chrysoscelis, Venkateshwar Mutyam, Matthew V. Puccetti, James Frisbie, David L. Goldstein, Carissa M. Krane

Biology Faculty Publications

Cope's gray treefrog, Hyla chrysoscelis, is a freeze-tolerant anuran that accumulates cryoprotective glycerol during cold acclimation. H. chrysoscelis erythrocytes express the aquaglyceroporin HC-3, which facilitates transmembrane glycerol and water movement. Aquaglyceroporins have no pharmacological inhibitors, and no genetic knockout tools currently exist for H. chrysoscelis. A phosphorodiamidate morpholino oligo (PMO)–mediated expression knockdown approach was therefore pursued to provide a model for testing the role of HC-3. We describe a novel procedure optimized for specific, efficient knockdown of HC-3 expression in amphibian erythrocyte suspensions cultured at nonmammalian physiological temperatures using Endo-Porter. Our protocol includes three critical components: pre-incubation at 37°C, …

Identification, Cloning And Characterization Of Van Operon In Cyanobacterium Synechococcus Sp. Iu 625, Robert Newby Jr.

Seton Hall University Dissertations and Theses (ETDs)

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Generation, Cloning, And Expression Of Full-Length Human Evc Gene, Trey Polvadore

Undergraduate Research Conference

No abstract provided.

Comparison Of Subcellular Responses For The Evaluation And Prediction Of The Chemotherapeutic Response To Cisplatin In Lung Adenocarcinoma Using Raman Spectroscopy, Haq Nawaz, Franck Bonnier, Aidan Meade, Fiona Lyng, Hugh Byrne

Articles

Confocal Raman Micro spectroscopy (CRM) is employed to examine the chemical and physiological effects of anticancer agents, using cisplatin and A549 adenocarcinoma cells as a model compound and test system respectively. Spectral responses of the membrane and cytoplasm of the cell are analysed independently and the results are compared to previously reported spectroscopic studies of the nucleus. Moreover, Raman spectra from the proteins extracted from the control and exposed samples are acquired and analysed to confirm the origin of the molecular changes of the cell membrane and cytoplasm of the A549 cells. Multivariate data analysis techniques including Principal Component Analysis …

Copyright For Engineered Dna: An Idea Whose Time Has Come?, Christopher M. Holman

West Virginia Law Review

The rapidly emerging field of synthetic biology has tremendous potential to address some of the most compelling challenges facing our planet by providing clean renewable energy, nutri- tionally-enhanced and environmentally friendly agricultural products, and revolutionary new life-saving cures. However, leaders in the synthetic biology movement have voiced concern that biotechnology's current patent-centric approach to intellec- tual property is in many ways ill-suited to meet the challenge of synthetic biology, threatening to impede follow-on innovation and open access technology. For years, copyright and patent protection for computer software have existed side-by-side, the two forms of intellectual property complementing one another. Numerous …

Sherley V. Sebelius: Stem Cells And The Uneasy Interplay Between The Federal Bench And The Lab Bench, Ryan P. O'Quinn

Duke Law & Technology Review

After Barack Obama's election to the presidency, he promised that one of his top priorities in office would be to relieve the restrictions initiated by President George W. Bush on federal funding of embryonic stem cell research. President Obama followed through on his promise, but the celebrations in the nation's research labs were short-lived. Anti-abortion advocates and other scientists working in the field that would allegedly be out-competed in the federal funding arena brought a legal challenge to the new government position. The struggle culminated in August 2010 with a federal district court issuing a preliminary injunction to halt the …

Pcr Primers For The Detection Of Propane And Butane-Oxidizing Microorganisms, Brian Jeremy Chan

Master's Theses

In an increasingly energy-hungry world, our capacity to meet the heightened energy demands of the future has become a pressing matter. The most urgent of these concerns are tied to the accessibility of petroleum. Various experts have proselytized both the imminent arrival of peak oil production rates and the ensuing decline of those rates thereafter. And to that end, the development of novel and advanced oil exploration methodologies has become almost as important as finding the sources of oil themselves.

The soils above petroleum reservoirs play host to various communities of alkane- oxidizing bacteria that can utilize the natural gas …

Bacterial Killing By Dry Metallic Copper Surfaces, Christophe Espírito Santo, Ee Wen Lam, Christian Elowsky, Davide Quaranta, Dylan W. Domaille, Christopher J. Chang, Gregor Grass

Nebraska Center for Biotechnology: Faculty and Staff Publications

Metallic copper surfaces rapidly and efficiently kill bacteria. Cells exposed to copper surfaces accumulated large amounts of copper ions, and this copper uptake was faster from dry copper than from moist copper. Cells suffered extensive membrane damage within minutes of exposure to dry copper. Further, cells removed from copper showed loss of cell integrity. Acute contact with metallic copper surfaces did not result in increased mutation rates or DNA lesions. These findings are important first steps for revealing the molecular sensitive targets in cells lethally challenged by exposure to copper surfaces and provide a scientific explanation for the use of …

Biophysical Characterization Of The Membrane Binding Domain Of The Pro-Apoptotic Protein Bax, Pranav Garg

Electronic Theses and Dissertations

The BCL-2 family of proteins tightly regulates the delicate balance between life and death. The pore forming Bax is a pro-apoptotic member belonging to this protein family. At the onset of apoptosis, monomeric cytoplasmic Bax translocates to the outer mitochondrial membrane, forms oligomeric pores thereby letting mitochondrial cytochrome c enter the cytosol and initiate the apoptotic cascade. The C-terminal "helix 9" is thought to mediate the membrane binding of BAX. A 20-amino acid peptide corresponding to Bax C-terminus (VTIFVAGVLTASLTIWKKMG) and two mutants where the two lysines are replaced with Glu (charge reversal mutant, EE) or Leu (charge neutralization mutant, LL) …

Quantitative Analysis Of Lignocellulosic Components Of Non-Treated And Steam Exploded Barley, Canola, Oat And Wheat Straw Using Fourier Transform Infrared Spectroscopy, P. K. Adapa, L. G. Schonenau, Thomas Canam, T. Dumonceaux

Faculty Research & Creative Activity

Rapid and cost effective quantification of lignocellulosic components (cellulose, hemicelluloses and lignin) of agricultural biomass (barley, canola, oat and wheat) is essential to determine the effect of various pre-treatments (such as steam explosion) on biomass used as feedstock for the biofuel industry. Fourier Transformed Infrared (FTIR) spectroscopy was considered as an option to achieve this objective. Regression equations having R2 values of 0.89, 0.99 and 0.98 were developed to predict the cellulose, hemicelluloses and lignin compounds of biomass, respectively. The average absolute difference in predicted and measured cellulose, hemicellulose and lignin in agricultural biomass was 7.5%, 2.5%, and 3.8%, respectively.

Quantitative Analysis Of Lignocellulosic Components Of Non-Treated And Steam Exploded Barley, Canola, Oat And Wheat Straw Using Fourier Transform Infrared Spectroscopy, P. Adapa, L. Schonenau, Thomas Canam, T. Dumonceaux

Faculty Research & Creative Activity

Rapid and cost effective quantification of lignocellulosic components (cellulose, hemicelluloses and lignin) of agricultural biomass (barley, canola, oat and wheat) is essential to determine the effect of various pre-treatments (such as steam explosion) on biomass used as feedstock for the biofuel industry. Fourier Transformed Infrared (FTIR) spectroscopy was considered as an option to achieve this objective. Regression equations having R2 values of 0.89, 0.99 and 0.98 were developed to predict the cellulose, hemicelluloses and lignin compounds of biomass, respectively. The average absolute difference in predicted and measured cellulose, hemicellulose and lignin in agricultural biomass was 7.5%, 2.5%, and 3.8%, respectively.

Chemical Characterization And In Vitro Fermentation Of Brassica Straw Treated With The Aerobic Fungus, Trametes Versicolor, J. E. Ramirez-Bribiesca, Y. Wang, L. Jin, Thomas Canam, J. R. Town, A. Tsang, T. J. Dumonceaux, T. A. Mcallister

Faculty Research & Creative Activity

Brassica napus straw (BNS) was either not treated or was treated with two strains of Trametes versicolor; 52J (wild type) or m4D (a cellobiose dehydrogenase-deficient mutant) with four treatments. Glucose was provided to encourage growth of the mutant strain. All treatments with T. versicolor decreased (P<0.05) neutral-detergent fibre and increased (P<0.05) protein and the concentration of lignin degradation products in straw. Ergosterol was highest (P<0.05) in straw treated with B-52J, suggesting it generated the most fungal biomass. Insoluble lignin was reduced (P<0.05) in straw treated with B-52J and B-m4D, but not with B-m4Dg. Mannose and xylose concentration were generally higher (P<0.05) in straw treated with fungi, whereas glucose and galactose were lower as compared with C-BNS. The four treatments above were subsequently assessed in rumen in vitro fermentations, along with BNS treated with 5 N NaOH. Concentrations of total volatile fatty acids after 24 and 48h were lower (P<0.05) in incubations that contained BNS treated with T. versicolor as compared with C-BNSor NaOH-treated BNS. Compared with C-BNS, in vitrodry matter disappearance and gas production were increased (P<0.05) by NaOH, but not by treatment with either strain of T. versicolor. Although treatment with T. versicolor did release more lignin degradation products, it did not appear to provide more degradable carbohydrate to in vitro rumen microbial populations, even when a mutant strain with compromised carbohydrate metabolism was utilized. Production of secondary compounds by the aerobic fungi may inhibit rumen microbial fermentation.

Linear Methods For Analysis And Quality Control Of Relative Expression Ratios From Quantitative Real-Time Polymerase Chain Reaction Experiments, Robert B. Page, Arnold J. Stromberg

Biology Faculty Publications

Relative expression quantitative real-time polymerase chain reaction (RT-qPCR) experiments are a common means of estimating transcript abundances across biological groups and experimental treatments. One of the most frequently used expression measures that results from such experiments is the relative expression ratio (R_E), which describes expression in experimental samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to one or more experimental or nonbaseline condition) in terms of fold change relative to calibrator samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to a control or baseline condition). Over the past decade, several …

Rotavirus Nsp4: Cell Type-Dependent Transport Kinetics To The Exofacial Plasma Membrane And Release From Intact Infected Cells, Thomas F. Gibbons, Stephen M. Storey, Cecelia V. Williams, Avery Mcintosh, Deanne M. Mitchel, Rebecca D. Parr, Friedhelm Schroeder, Judith M. Ball

Faculty Publications

Background

Rotavirus NSP4 localizes to multiple intracellular sites and is multifunctional, contributing to RV morphogenesis, replication and pathogenesis. One function of NSP4 is the induction of early secretory diarrhea by binding surface receptors to initiate signaling events. The aims of this study were to determine the transport kinetics of NSP4 to the exofacial plasma membrane (PM), the subsequent release from intact infected cells, and rebinding to naïve and/or neighboring cells in two cell types.

Methods

Transport kinetics was evaluated using surface-specific biotinylation/streptavidin pull-downs and exofacial exposure of NSP4 was confirmed by antibody binding to intact cells, and fluorescent resonant energy …

Chemical Characterization And In Vitro Fermentation Of Brassica Straw Treated With The Aerobic Fungus, Trametes Versicolor, J. Ramirez-Bribiesca, Y. Wang, L. Jin, Thomas Canam, J. Town, A. Tsang, T. Dumonceaux, T. Mcallister

Faculty Research & Creative Activity

Brassica napus straw (BNS) was either not treated or was treated with two strains of Trametes versicolor; 52J (wild type) or m4D (a cellobiose dehydrogenase-deficient mutant) with four treatments. Glucose was provided to encourage growth of the mutant strain. All treatments with T. versicolor decreased (P<0.05) neutral-detergent fibre and increased (P<0.05) protein and the concentration of lignin degradation products in straw. Ergosterol was highest (P<0.05) in straw treated with B-52J, suggesting it generated the most fungal biomass. Insoluble lignin was reduced (P<0.05) in straw treated with B-52J and B-m4D, but not with B-m4Dg. Mannose and xylose concentration were generally higher (P<0.05) in straw treated with fungi, whereas glucose and galactose were lower as compared with C-BNS. The four treatments above were subsequently assessed in rumen in vitro fermentations, along with BNS treated with 5 N NaOH. Concentrations of total volatile fatty acids after 24 and 48h were lower (P<0.05) in incubations that contained BNS treated with T. versicolor as compared with C-BNSor NaOH-treated BNS. Compared with C-BNS, in vitrodry matter disappearance and gas production were increased (P<0.05) by NaOH, but not by treatment with either strain of T. versicolor. Although treatment with T. versicolor did release more lignin degradation products, it did not appear to provide more degradable carbohydrate to in vitro rumen microbial populations, even when a mutant strain with compromised carbohydrate metabolism was utilized. Production of secondary compounds by the aerobic fungi may inhibit rumen microbial fermentation.

Biological Activity And Mass Spectrometric Analysis Of Vernonia Amygdalina Fractions, Broderick Eribo

Department of Biology Faculty Publications

Vernonia amygdalina (VA) is a tropical African plant of the Asteraceae family used as dietary supplement and as a medicinal herb. In this study, fatty acid esters, fatty acid amide, triterpene, diterpene alcohols and phytostanols were identified as the major chemical groups in the aqueous and organic fractions of VA leaf extracts. Their structures were elucidated, on the basis of GC-MS data, as hexanedioic acid, bis (2-ethylhexyl) ester (2a), erucamide (2b) and squalene (2c) in the water fraction; hexadecanoic acid methyl ester (3a), 9(Z)12(Z)15(Z)-octadecatrienoic acid, methyl ester (3b) and phytol (3c) in methanol fraction; phytol (4a), squalene (4b) and 7,22-ergostadienol …

Mne1 Is A Novel Component Of The Mitochondrial Splicing Apparatus Responsible For Processing Of A Cox1 Group I Intron In Yeast, Talina Watts, Oleh Khalimonchuk, Rachel Z. Wolf, Edward M. Turk, Georg Mohr, Dennis R. Winge

Department of Biochemistry: Faculty Publications

Saccharomyces cerevisiae cells lacking Mne1 are deficient in

intron splicing in the gene encoding the Cox1 subunit of cytochrome

oxidase but contain wild-type levels of the bc1 complex.

Thus, Mne1 has no role in splicing of COB introns or expression

of the COB gene. Northern experiments suggest that splicing of

the COX1 aI5β intron is dependent on Mne1 in addition to the

previously known Mrs1, Mss116, Pet54, and Suv3 factors. Processing

of the aI5_ intron is similarly impaired in mne1∆ and

mrs1∆ cells and overexpression of Mrs1 partially restores the

respiratory function of mne1∆ cells. Mrs1 …

Hydrogen Peroxide Probes Directed To Different Cellular Compartments, Mikalai Malinouski, You Zhou, Vsevolod V. Belousov, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Background: Controlled generation and removal of hydrogen peroxide play important roles in cellular redox homeostasis and signaling. We used a hydrogen peroxide biosensor HyPer, targeted to different compartments, to examine these processes in mammalian cells.

Principal Findings: Reversible responses were observed to various redox perturbations and signaling events. HyPer expressed in HEK 293 cells was found to sense low micromolar levels of hydrogen peroxide. When targeted to various cellular compartments, HyPer occurred in the reduced state in the nucleus, cytosol, peroxisomes, mitochondrial intermembrane space and mitochondrial matrix, but low levels of the oxidized form of the biosensor were also observed …

Reduced Utilization Of Selenium By Naked Mole Rats Due To A Specific Defect In Gpx1 Expression, Marina V. Kasaikina, Alexei V. Lobanov, Mikalai I. Malinouski, Byung Cheon Lee, Javier Seravalli, Dmitri E. Fomenko, Anton A. Turanov, Lydia Finney, Stefan Vogt, Thomas J. Park, Richard A. Miller, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Naked mole rat (MR) Heterocephalus glaber is a rodent model of delayed aging because of its unusually long life span (>28 years). It is also not known to develop cancer. In the current work, tissue imaging by x-ray fluorescence microscopy and direct analyses of trace elements revealed low levels of selenium in the MR liver and kidney, whereas MR and mouse brains had similar selenium levels. This effect was not explained by uniform selenium deficiency because methionine sulfoxide reductase activities were similar in mice and MR. However, glutathione peroxidase activity was an order of magnitude lower inMRliver and kidney …