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Maintenance Of The Ph Gradient In The Gastric Mucus Layer., Owen Lewis 2016 The University Of Utah

Maintenance Of The Ph Gradient In The Gastric Mucus Layer., Owen Lewis

Annual Symposium on Biomathematics and Ecology: Education and Research

No abstract provided.


Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat 2016 University of Alberta

Microfluidic Cantilever Detects Bacteria And Measures Their Susceptibility To Antibiotics In Small Confined Volumes, Hashem Etayash, M. F. Khan, Kamaljit Kaur, Thomas Thundat

Pharmacy Faculty Articles and Research

In the fight against drug-resistant bacteria, accurate and high-throughput detection is essential. Here, a bimaterial microcantilever with an embedded microfluidic channel with internal surfaces chemically or physically functionalized with receptors selectively captures the bacteria passing through the channel. Bacterial adsorption inside the cantilever results in changes in the resonance frequency (mass) and cantilever deflection (adsorption stress). The excitation of trapped bacteria using infrared radiation (IR) causes the cantilever to deflect in proportion to the infrared absorption of the bacteria, providing a nanomechanical infrared spectrum for selective identification. We demonstrate the in situ detection and discrimination of Listeria monocytogenes at a ...


Structural Determinants Allowing Transferase Activity In Sensitive To Freezing 2, Classified As A Family I Glycosyl Hydrolase, Rebecca Roston, Kun Wang, Leslie A. Kuhn, Christoph Benning 2016 University of Nebraska- Lincoln

Structural Determinants Allowing Transferase Activity In Sensitive To Freezing 2, Classified As A Family I Glycosyl Hydrolase, Rebecca Roston, Kun Wang, Leslie A. Kuhn, Christoph Benning

Biochemistry -- Faculty Publications

Background: SENSITIVE TO FREEZING 2 (SFR2) is classified as a glycosyl hydrolase, and by using glycosyltransferase activity, it modifies membrane lipids to promote freeze tolerance.

Results: Although the active site of SFR2 is identical to hydrolases, adjacent loop regions contribute to its transferase activity.

Conclusion: Transferase activity evolved by modifications external to the core catalytic site.

Significance: Defined structure-function relationships will inform engineering of transferases and freeze tolerance.


Sending Out An Sos: Mitochondria As A Signaling Hub, Iryna Bohovych, Oleh Khalimonchuk 2016 University of Nebraska- Lincoln

Sending Out An Sos: Mitochondria As A Signaling Hub, Iryna Bohovych, Oleh Khalimonchuk

Biochemistry -- Faculty Publications

Normal cellular physiology is critically dependent on numerous mitochondrial activities including energy conversion, cofactor and precursor metabolite synthesis, and regulation of ion and redox homeostasis. Advances in mitochondrial research during the last two decades provide solid evidence that these organelles are deeply integrated with the rest of the cell and multiple mechanisms are in place to monitor and communicate functional states of mitochondria. In many cases, however, the exact molecular nature of various mitochondria-to-cell communication pathways is only beginning to emerge. Here, we review various signals emitted by distressed or dysfunctional mitochondria and the stress-responsive pathways activated in response to ...


In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne 2016 Dublin Institute of Technology

In Vitro Monitoring Of Time And Dose Dependent Cytotoxicity Of Aminated Nanoparticles Using Raman Spectroscopy, Esen Efeoglu, Alan Casey, Hugh Byrne

Articles

No abstract provided.


Small-Angle X-Ray Scattering Studies Of The Oligomeric State And Quaternary Structure Of The Trifunctional Proline Utilization A (Puta) Flavoprotein From Escherichia Coli, Ranjan K. Singh, John D. Larson, Weidong Zhu, Robert P. Rambo, Greg L. Hura, Donald F. Becker, John J. Tanner 2016 University of Missouri-Columbia

Small-Angle X-Ray Scattering Studies Of The Oligomeric State And Quaternary Structure Of The Trifunctional Proline Utilization A (Puta) Flavoprotein From Escherichia Coli, Ranjan K. Singh, John D. Larson, Weidong Zhu, Robert P. Rambo, Greg L. Hura, Donald F. Becker, John J. Tanner

Biochemistry -- Faculty Publications

Background: Trifunctional proline utilization A (PutA) proteins are multifunctional flavoproteins that catalyze two reactions and repress transcription of the put regulon.

Results: PutA from Escherichia coli is a V-shaped dimer, with the DNA-binding domain mediating dimerization.

Conclusion: Oligomeric state and quaternary structures are not conserved by PutAs.

Significance: The first three-dimensional structural information for any trifunctional PutA is reported.


Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal 2016 University of Connecticut

Computational Investigations Into The Molecular Underpinnings Of Eyesight Signaling Pathways, Shaan Kamal

University Scholar Projects

Phosphodiesterase 6 (PDE6) is a critical enzyme in the eyesight-signaling pathway. When activated, PDE6 hydrolyzes cGMP to GMP, which deactivates cGMP- gated ion channels, causing hyperpolarization of the cell and activating the sensory neurons responsible for vision. Within the PDE family, PDE6 is the only enzyme known to have an inhibitory subunit (PDE6-γ), which allows for the regulation of cGMP levels. When PDE6-γ is bound to PDE6, the enzyme is turned “off” and cannot catalyze cGMP. The α subunit of the G-protein transducin removes PDE6-γ and activates PDE6. PDE6 has proven problematic to isolate, making it difficult to study experimentally ...


Modulation Of Cell Death Signaling And Cell Proliferation By The Interaction Of Homoserine Lactones And Paraoxonase 2., Aaron Mackallan Neely 2016 University of Louisville

Modulation Of Cell Death Signaling And Cell Proliferation By The Interaction Of Homoserine Lactones And Paraoxonase 2., Aaron Mackallan Neely

Electronic Theses and Dissertations

Pseudomonas aeruginosa produces N-(3-oxododecanoyl)-homoserine lactone (C12) as a quorum-sensing molecule that functions to facilitate bacteria-bacteria communication. C12 has also been reported to affect many aspects of human host cell physiology, including evoking cell death in various types of cells. However, the signaling pathway(s) leading to C12-triggerred cell death remains unclear. To clarify cell death signaling induced by C12, we examined mouse embryonic fibroblasts (MEFs) deficient in one or more caspases. Our data indicate that, unlike most apoptotic inducers, C12 evokes a novel form of apoptosis in cells, probably through the direct induction of mitochondrial membrane permeabilization. Previous ...


Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel 2016 University of Arkansas, Fayetteville

Engineering A Mutation In The Heparin Binding Pocket Of The Human Fibroblast Growth Factor, Roshni Patel

Chemistry & Biochemistry Undergraduate Honors Theses

Fibroblast growth factors (FGFs) are family of proteins that belong to a group of growth factors that are found in mammals and play an important role in angiogenesis, differentiation, organogenesis, and tissue repair. In summary, their main functionality is involved in cell division and proliferation. Because FGFs plays such a vital role in cell proliferation, they are mainly involved in the process of wound healing and injuries. FGF binds to its ligand, heparin—a heavily sulfated glycosaminoglycan. The binding of heparin to FGF occurs through electrostatic interactions, specifically between the negatively charged sulfate groups on heparin and positively charged residues ...


Assessment Of Calcein Dye Method To Observe Cell Volume Regulation, Danielle M. Precourt 2016 Buffalo State College

Assessment Of Calcein Dye Method To Observe Cell Volume Regulation, Danielle M. Precourt

Forensic Science Theses

Cell volume regulation (CVR) is a crucial mechanism for the maintenance of homeostasis of cells under significant osmotic challenges. When cells are swollen or shrunken in a non-isotonic medium they initiate a regulatory mechanism to restore to their initial volume. Swollen cells in a hypotonic solution show decreases in cell volume by releasing osmolytes and water, through a regulatory volume decrease (RVD) mechanism. On the contrary, shrunken cells in a hypertonic solution exhibit a regulatory volume increase (RVI) by up-taking osmolytes and water. The whole process of CVR is complicated and involves diverse cell sensory mechanisms of a volume change ...


Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu 2016 University of Tennessee - Knoxville

Complex Non-Equilibrium Structural Dynamics In Globular Proteins, Xiaohu Hu

Doctoral Dissertations

Internal structural motions in proteins are essential to their functions. In this present dissertation, we present the results from an extensive set of molecular dynamics simulations of three very different globular proteins and demonstrate that the structural fluctuations observed are highly complex, manifesting in non-ergodic and self-similar subdiffusive dynamics with non-exponential relaxation behavior. The characteristic time of the motion observed at a given timescale is dependent on the length of the observation time, indicating an aging effect. By comparing the simulation results to the existing single-molecule fluorescence spectroscopic data on other globular proteins, we found the characteristic relaxation time for ...


Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters 2016 Western Michigan University

Effects Of Creatine, Leucine, And Ethanol On Glial Cell Line-Derived Neurotrophic Factor In C2c12 Skeletal Muscle Cells, Daniel Waters

Honors Theses

Glial Cell Line-Derived Neurotrophic Factor (GDNF) is a protein expressed throughout the mammalian nervous system that serves several protective functions. Originally discovered in the brain, where it supports the survival of dopaminergic neurons, GDNF has since been shown to be expressed in skeletal muscle and is vital for the maintenance of motor neurons. The relationship between muscle hypertrophy, and GDNF is not well understood. The purpose of this study was to examine the relationship between hypertrophy and GDNF by inducing hypertrophy in C2C12 skeletal muscle cells using leucine and creatine, inhibiting hypertrophy using ethanol and measuring GDNF content. As measured ...


The Hmut Protein In The Heme Uptake Pathway Of Corynebacterium Diphtheriae, Cyrianne Sonia Keutcha 2016 Georgia State University

The Hmut Protein In The Heme Uptake Pathway Of Corynebacterium Diphtheriae, Cyrianne Sonia Keutcha

Georgia State Undergraduate Research Conference

No abstract provided.


Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan 2016 University of Nebraska-Lincoln

Methods For Detecting Microbial Methane Production And Consumption By Gas Chromatography, Jared T. Aldridge, Jennie L. Catlett, Megan L. Smith, Nicole R. Buan

Biochemistry -- Faculty Publications

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al., 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al., 2015). Here we describe the end point and kinetic ...


Stabilin-1 And Stabilin-2 Are Specific Receptors For The Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos) In The Liver, Colton M. Miller, Aaron J. Donnerr, Emma E. Blank, Andrew W. Egger, Brianna M. Kellar, Michael E. Østergaard, Punit P. Seth, Edward N. Harris 2016 University of Nebraska- Lincoln

Stabilin-1 And Stabilin-2 Are Specific Receptors For The Cellular Internalization Of Phosphorothioate-Modified Antisense Oligonucleotides (Asos) In The Liver, Colton M. Miller, Aaron J. Donnerr, Emma E. Blank, Andrew W. Egger, Brianna M. Kellar, Michael E. Østergaard, Punit P. Seth, Edward N. Harris

Biochemistry -- Faculty Publications

Phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) have been extensively investigated over the past three decades as pharmacological and therapeutic agents. One second generation ASO, KynamroTM, was recently approved by the FDA for the treatment of homozygous familial hypercholesterolemia and over 35 second generation PS ASOs are at various stages of clinical development. In this report, we show that the Stabilin class of scavenger receptors, which were not previously thought to bind DNA, do bind and internalize PS ASOs. With the use of primary cells from mouse and rat livers and recombinant cell lines each expressing Stabilin-1 and each isoform ...


Systems Perturbation Analysis Of A Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates For Cancer Therapeutics, Bhanwar Lal Puniya, Laura Allen, Colleen Hochfelde, Mahbubul Majumder, Tomáš Helikar 2016 University of Nebraska-Lincoln

Systems Perturbation Analysis Of A Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates For Cancer Therapeutics, Bhanwar Lal Puniya, Laura Allen, Colleen Hochfelde, Mahbubul Majumder, Tomáš Helikar

Biochemistry -- Faculty Publications

Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical components that could be further explored as therapeutic targets. Here, we performed perturbation analysis of a large-scale signal transduction model in extracellular environments that stimulate cell death, growth, motility, and quiescence. Each of the model's components was perturbed under both loss-of-function and gain-of-function mutations. Using 1,300 simulations under both types of perturbations across various extracellular conditions, we identified the most and least influential components ...


Regulation Of Dj-1 By Glutaredoxin 1 In Vivo – Implications For Parkinson’S Disease, William M. Johnson, Marcin Golczak, Kyonghwan Choe, Pierce L. Curran, Olga Gorelenkova Miller, Chen Yao, Wenzhang Wang, Jiusheng Lin, Nicole M. Milkovic, Ajit Ray, Vijayalakshmi Ravindranath, Xiongwei Zhu, Mark A. Wilson, Amy L. Wilson-Delfosse, Shu G. Chen, John J. Mieyal 2016 Case Western Reserve University

Regulation Of Dj-1 By Glutaredoxin 1 In Vivo – Implications For Parkinson’S Disease, William M. Johnson, Marcin Golczak, Kyonghwan Choe, Pierce L. Curran, Olga Gorelenkova Miller, Chen Yao, Wenzhang Wang, Jiusheng Lin, Nicole M. Milkovic, Ajit Ray, Vijayalakshmi Ravindranath, Xiongwei Zhu, Mark A. Wilson, Amy L. Wilson-Delfosse, Shu G. Chen, John J. Mieyal

Biochemistry -- Faculty Publications

Parkinson’s disease (PD) is the second most common neurodegenerative disease worldwide, caused by the degeneration of the dopaminergic neurons in the substantia nigra. Mutations in PARK7 (DJ-1) result in early onset autosomal recessive PD, and oxidative modification of DJ-1 has been reported to regulate the protective activity of DJ-1 in vitro. Glutathionylation is a prevalent redox modification of proteins resulting from the disulfide adduction of the glutathione moiety to a reactive cysteine-SH; and glutathionylation of specific proteins has been implicated in regulation of cell viability. Glutaredoxin 1 (Grx1) is the principal deglutathionylating enzyme within cells, and it has been ...


Pluralistic And Stochastic Gene Regulation: Examples, Models And Consistent Theory, Elisa N. Salas, Jiang Shu, Matyas F. Cserhati, Donald P. Weeks, Istvan Ladunga 2016 University of Nebraska-Lincoln

Pluralistic And Stochastic Gene Regulation: Examples, Models And Consistent Theory, Elisa N. Salas, Jiang Shu, Matyas F. Cserhati, Donald P. Weeks, Istvan Ladunga

Biochemistry -- Faculty Publications

We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of transcription factors, variable DNA motifs, and bursts in gene expression. Stochastic regulation is also indicated by frequently subdued effects of knockout mutants of regulators, their evolutionary losses/gains and massive rewiring of regulatory sites. We report wide-spread pluralistic regulation in ≈800 000 tightly co-expressed pairs of diverse human genes. Typically, half of ≈50 observed regulators bind to ...


Inhibiting Hexamer Disassembly Of Human Udp-Glucose Dehydrogenase By Photoactivated Amino Acid Crosslinking, George Grady, Ashley Thelen, Jaleen Albers, Tong Ju, Jiantao Guo, Joseph J. Barycki, Melanie A. Simpson 2016 University of Nebraska-Lincoln

Inhibiting Hexamer Disassembly Of Human Udp-Glucose Dehydrogenase By Photoactivated Amino Acid Crosslinking, George Grady, Ashley Thelen, Jaleen Albers, Tong Ju, Jiantao Guo, Joseph J. Barycki, Melanie A. Simpson

Biochemistry -- Faculty Publications

The enzyme UDP-glucose dehydrogenase (UGDH) catalyzes the reaction of UDP-glucose to UDP-glucuronate through two successive NAD+-dependent oxidation steps. Human UGDH apoprotein purifies as a mixture of dimeric and hexameric species. Addition of substrate and cofactor stabilizes the oligomeric state to primarily the hexameric form. To determine if the dynamic conformations of hUGDH are required for catalytic activity, we used site-specific unnatural amino acid incorporation to facilitate crosslinking of monomeric subunits into predominantly obligate oligomeric species. Optimal crosslinking was achieved by encoding p-benzoyl-L-phenylalanine at position 458, normally a glutamine located within the dimer-dimer interface, and exposing to long wavelength UV ...


Loss Of Exogenous Androgen Dependence By Prostate Tumor Cells Is Associated With Elevated Glucuronidation Potential, Brenna M. Zimmer, Michelle E. Howell, Qin Wei, Linlin Ma, Trevor Romsdahl, Eileen G. Loughman, Jonathan E. Markham, Javier Seravalli, Joseph J. Barycki, Melanie A. Simpson 2016 University of Nebraska-Lincoln

Loss Of Exogenous Androgen Dependence By Prostate Tumor Cells Is Associated With Elevated Glucuronidation Potential, Brenna M. Zimmer, Michelle E. Howell, Qin Wei, Linlin Ma, Trevor Romsdahl, Eileen G. Loughman, Jonathan E. Markham, Javier Seravalli, Joseph J. Barycki, Melanie A. Simpson

Biochemistry -- Faculty Publications

Prostate epithelial cells control the potency and availability of androgen hormones in part by inactivation and elimination. UDP-glucose dehydrogenase (UGDH) catalyzes the NAD+-dependent oxidation of UDP-glucose to UDP-glucuronate, an essential precursor for androgen inactivation by the prostate glucuronidation enzymes UGT2B15 and UGT2B17. UGDH expression is androgen stimulated, which increases the production of UDP-glucuronate, and fuels UGT-catalyzed glucuronidation. In this study, we compared the glucuronidation potential and its impact on androgen-mediated gene expression in an isogenic LNCaP model for androgen dependent versus castration resistant prostate cancer. Despite significantly lower androgen-glucuronide output, LNCaP 81 castration resistant tumor cells expressed higher levels ...


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