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Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant Ovarian Cancer, Canan Schumann, Stephanie Chan, Oleh Khalimonchuk, Shannon Khal, Vitaliya Moskal, Vidhi Shah, Adam W. G. Alani, Olena Taratula, Oleh Taratula 2016 Oregon State University

Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant Ovarian Cancer, Canan Schumann, Stephanie Chan, Oleh Khalimonchuk, Shannon Khal, Vitaliya Moskal, Vidhi Shah, Adam W. G. Alani, Olena Taratula, Oleh Taratula

Biochemistry -- Faculty Publications

We report an efficient therapeutic modality for platinum resistant ovarian cancer based on siRNAmediated suppression of a multifunctional DJ-1 protein that is responsible for the proliferation, growth, invasion, oxidative stress and overall survival of various cancers. The developed therapeutic strategy can work alone or in concert with a low dose of the first line chemotherapeutic agent cisplatin, to elicit a maximal therapeutic response. To achieve an efficient DJ-1 knockdown, we constructed the polypropylenimine dendrimer-based nanoplatform targeted to LHRH receptors overexpressed on ovarian cancer cells. The quantitative PCR and western immunoblotting analysis, revealed that the delivered DJ-1 siRNA downregulated the expression ...


Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Ed Harris 2016 University of Nebraska- Lincoln

Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Ed Harris

Biochemistry -- Faculty Publications

The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for ...


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 ...


Synthesis And Transfer Of Galactolipids In The Chloroplast Envelope Membranes Of Arabidopsis Thaliana, Amélie Kelly, Barbara Kalisch, Georg Hölzl, Sandra Schulze, Juliane Thiele, Michael Melzer, Rebecca L. Roston, Christoph Benning, Peter Dörmann 2016 Max Planck Institute of Molecular Plant Physiology

Synthesis And Transfer Of Galactolipids In The Chloroplast Envelope Membranes Of Arabidopsis Thaliana, Amélie Kelly, Barbara Kalisch, Georg Hölzl, Sandra Schulze, Juliane Thiele, Michael Melzer, Rebecca L. Roston, Christoph Benning, Peter Dörmann

Biochemistry -- Faculty Publications

Galactolipids [monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol

(DGDG)] are the hallmark lipids of photosynthetic

membranes. The galactolipid synthases MGD1 and DGD1

catalyze consecutive galactosyltransfer reactions but localize to the

inner and outer chloroplast envelopes, respectively, necessitating

intermembrane lipid transfer. Here we show that the N-terminal

sequence of DGD1 (NDGD1) is required for galactolipid transfer

between the envelopes. Different diglycosyllipid synthases (DGD1,

DGD2, and Chloroflexus glucosyltransferase) were introduced into

the dgd1-1 mutant of Arabidopsis in fusion with N-terminal extensions

(NDGD1 and NDGD2) targeting to the outer envelope. Reconstruction

of DGDG synthesis in the outer envelope membrane was

observed only with diglycosyllipid synthase fusion ...


Alcoholic Vs Non-Alcoholic Fatty Liver In Rats: Distinct Differences In Endocytosis And Vesicle Trafficking Despite Similar Pathology, Karuna Rasineni, Daniel D. Penrice, Sathish Kumar Natarajan, Mark A. McNiven, Benita L. McVicker, Kusum K. Kharbanda, Carol A. Casey, Edward N. Harris 2016 University of Nebraska Medical Center

Alcoholic Vs Non-Alcoholic Fatty Liver In Rats: Distinct Differences In Endocytosis And Vesicle Trafficking Despite Similar Pathology, Karuna Rasineni, Daniel D. Penrice, Sathish Kumar Natarajan, Mark A. Mcniven, Benita L. Mcvicker, Kusum K. Kharbanda, Carol A. Casey, Edward N. Harris

Biochemistry -- Faculty Publications

Background: Non-alcoholic and alcoholic fatty liver disease (NAFLD and AFLD, respectively) are major health problems, as patients with either condition can progress to hepatitis, fibrosis, and cirrhosis. Although histologically similar, key differences likely exist in these two models. For example, altered content of several vesicle trafficking proteins have been identified in AFLD, but their content in NAFLD is unknown. In this study, we compared select parameters in NAFLD and AFLD in a rat model.

Methods: We fed either Lieber- DeCarli liquid control or alcohol-containing (35 % as calories) diet (AFLD model) or lean or high-fat (12 or 60 % derived from fat ...


Activation Of Erk And Nf-Κb During Hare-Mediated Heparin Uptake Require Only One Of The Four Endocytic Motifs, Madhu S. Pandey, Colton M. Miller, Edward N. Harris, Paul H. Weigel 2016 University of Oklahoma Health Sciences Center

Activation Of Erk And Nf-Κb During Hare-Mediated Heparin Uptake Require Only One Of The Four Endocytic Motifs, Madhu S. Pandey, Colton M. Miller, Edward N. Harris, Paul H. Weigel

Biochemistry -- Faculty Publications

Fifteen different ligands, including heparin (Hep), are cleared from lymph and blood by the Hyaluronan (HA) Receptor for Endocytosis (HARE; derived from Stabilin-2 by proteolysis), which contains four endocytic motifs (M1-M4). Endocytosis of HARE•Hep complexes is targeted to coated pits by M1, M2, and M3 (Pandey et al, Int. J. Cell Biol. 2015, article ID 524707), which activates ERK1/2 and NF-κB (Pandey et al J. Biol. Chem. 288, 14068–79, 2013). Here, we used a NF-κB promoter-driven luciferase gene assay and cell lines expressing different HARE cytoplasmic domain mutants to identify motifs needed for Hepmediated signaling. Deletion of ...


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 ...


Fatty Acid Transport Proteins: Targeting Fatp2 As A Gatekeeper Involved In The Transport Of Exogenous Fatty Acids, Paul N. Black, Constance Ahowesso, David Montefusco, Nipun Saini, Concetta C. DiRusso 2016 University of Nebraska-Lincoln

Fatty Acid Transport Proteins: Targeting Fatp2 As A Gatekeeper Involved In The Transport Of Exogenous Fatty Acids, Paul N. Black, Constance Ahowesso, David Montefusco, Nipun Saini, Concetta C. Dirusso

Biochemistry -- Faculty Publications

The fatty acid transport proteins (FATP) are classified as members of the solute carrier 27 (Slc27) family of proteins based on their ability to function in the transport of exogenous fatty acids. These proteins, when localized to the plasma membrane or at intracellular membrane junctions with the endoplasmic reticulum, function as a gate in the regulated transport of fatty acids and thus represent a therapeutic target to delimit the acquisition of fatty acids that contribute to disease as in the case of fatty acid overload. To date, FATP1, FATP2, and FATP4 have been used as targets in the selection of ...


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 ...


Role Of Apoptotic Hepatocytes In Hcv Dissemination: Regulation By Acetaldehyde, Murali Ganesan, Sathish Kumar Natarajan, Jinjin Zhang, Justin L. Mott, Larisa I. Poluektova, Benita L. McVicker, Kusum K. Kharbanda, Dean J. Tuma, Natalie A. Osna 2016 Veterans Affairs Nebraska-Western Iowa Health Care System

Role Of Apoptotic Hepatocytes In Hcv Dissemination: Regulation By Acetaldehyde, Murali Ganesan, Sathish Kumar Natarajan, Jinjin Zhang, Justin L. Mott, Larisa I. Poluektova, Benita L. Mcvicker, Kusum K. Kharbanda, Dean J. Tuma, Natalie A. Osna

Biochemistry -- Faculty Publications

Alcohol consumption exacerbates hepatitis C virus (HCV) pathogenesis and promotes disease progression, although the mechanisms are not quite clear. We have previously observed that acetaldehyde (Ach) continuously produced by the acetaldehyde-generating system (AGS), temporarily enhanced HCV RNA levels, followed by a decrease to normal or lower levels, which corresponded to apoptosis induction. Here, we studied whether Ach-induced apoptosis caused depletion of HCV-infected cells and what role apoptotic bodies (AB) play in HCV-alcohol crosstalk. In liver cells exposed to AGS, we observed the induction of miR-122 and miR-34a. As miR-34a has been associated with apoptotic signaling and miR-122 with HCV replication ...


Evidence For Pipecolate Oxidase In Mediating Protection Against Hydrogen Peroxide Stress, Sathish Kumar Natarajan, Ezhumalai Muthukrishnan, Oleh Khalimonchuk, Justin L. Mott, Donald F. Becker 2016 University of Nebraska - Lincoln

Evidence For Pipecolate Oxidase In Mediating Protection Against Hydrogen Peroxide Stress, Sathish Kumar Natarajan, Ezhumalai Muthukrishnan, Oleh Khalimonchuk, Justin L. Mott, Donald F. Becker

Biochemistry -- Faculty Publications

Pipecolate, an intermediate of the lysine catabolic pathway, is oxidized to Δ1-piperideine-6-carboxylate (P6C) by the flavoenzyme lpipecolate oxidase (PIPOX). P6C spontaneously hydrolyzes to generate α-aminoadipate semialdehyde, which is then converted into α-aminoadipate acid by α-aminoadipatesemialdehyde dehydrogenase. l-pipecolate was previously reported to protect mammalian cells against oxidative stress. Here, we examined whether PIPOX is involved in the mechanism of pipecolate stress protection. Knockdown of PIPOX by small interference RNA abolished pipecolate protection against hydrogen peroxide-induced cell death in HEK293 cells suggesting a critical role for PIPOX. Subcellular fractionation analysis showed that PIPOX is localized in the mitochondria of HEK293 ...


Ceramide Induces Human Hepcidin Gene Transcription Through Jak/Stat3 Pathway, Sizhao Lu, Sathish Kumar Natarajan, Justin L. Mott, Kusum K. Kharbanda, Duygu Dee Harrison-Findik 2016 University of Nebraska Medical Center

Ceramide Induces Human Hepcidin Gene Transcription Through Jak/Stat3 Pathway, Sizhao Lu, Sathish Kumar Natarajan, Justin L. Mott, Kusum K. Kharbanda, Duygu Dee Harrison-Findik

Biochemistry -- Faculty Publications

Changes in lipid metabolism and iron content are observed in the livers of patients with fatty liver disease. The expression of hepcidin, an iron-regulatory and acute phase protein synthesized by the liver, is also modulated. The potential interaction of lipid and iron metabolism is largely unknown.We investigated the role of lipid intermediate, ceramide in the regulation of human hepcidin gene, HAMP. Human hepatoma HepG2 cells were treated with cell-permeable ceramide analogs. Ceramide induced significant up-regulation of HAMP mRNA expression in HepG2 cells. The effect of ceramide on HAMP expression was mediated through transcriptional mechanisms because it was completely blocked ...


Important Interactions Promoting Recognition Of Peptide Ligands At The Binding Pocket Of The Pdz Signaling Domain Of Af6, Quy (Rita) L. Tat 2016 University of Colorado Boulder

Important Interactions Promoting Recognition Of Peptide Ligands At The Binding Pocket Of The Pdz Signaling Domain Of Af6, Quy (Rita) L. Tat

Undergraduate Honors Theses

Afadin (AF6) is a scaffolding protein involved in the formation of protein complexes at tight and adherens junctions. AF6 plays vital roles in many cellular processes, such as structural development, cellular organization, directional cell movement, and polarity. The PDZ domain participates in multiple signaling networks to initiate and maintain cellular polarity, to facilitate protein trafficking, and allow neuronal communications; thus, misregulated PDZ domain-dependent pathways can induce cells to become cancerous. AF6 interacts with many other proteins via its PDZ signaling domain and exhibits multimodal specificity.

The PDZ signaling domain of AF6 (AF6_PDZ) binds predominantly hydrophobic peptide ligands. A biological array ...


Contributions Of Sequence And Structure To Ligand Selectivity In Class Ii Cobalamin Riboswitches, Samantha M. Webster 2016 Student

Contributions Of Sequence And Structure To Ligand Selectivity In Class Ii Cobalamin Riboswitches, Samantha M. Webster

Undergraduate Honors Theses

Riboswitches are gene regulatory elements found in the 5’-untranslated region of many bacterial genes. The direct binding of small molecule ligands induces conformational changes in the RNA that influence downstream expression machinery and determine the transcription or translation of an attached gene. Cobalamin riboswitches, which bind coenzyme-B12 and other cobalamin variants, are divided into two distinct classes. Cbl-I riboswitches contain a large peripheral element that limits riboswitch binding to only coenzyme-B12 (adenosylcobalamin, or AdoCbl). Cbl-II riboswitches do not contain the same peripheral element, and were originally thought to only bind smaller species of cobalamin (including methylcobalamin, or ...


Inactivation Of Cytomegalovirus In Breast Milk Using Ultraviolet-C Irradiation: Opportunities For A New Treatment Option In Breast Milk Banking, Megan L. Lloyd, Nurul Hod, Jothsna Jayaraman, Elizabeth A. Marchant, Lukas Christen, Peter Chiang, Peter E. Hartmann, Geoffrey R. Shellam, Karen N. Simmer 2016 University of Western Australia/Edith Cowan University

Inactivation Of Cytomegalovirus In Breast Milk Using Ultraviolet-C Irradiation: Opportunities For A New Treatment Option In Breast Milk Banking, Megan L. Lloyd, Nurul Hod, Jothsna Jayaraman, Elizabeth A. Marchant, Lukas Christen, Peter Chiang, Peter E. Hartmann, Geoffrey R. Shellam, Karen N. Simmer

ECU Publications Post 2013

Pasteurized donor human milk is provided by milk banks to very preterm babies where their maternal supply is insufficient or unavailable. Donor milk is currently processed by Holder pasteurization, producing a microbiologically safe product but significantly reducing immunoprotective components. Ultraviolet-C (UV-C) irradiation at 254 nm is being investigated as an alternative treatment method and has been shown to preserve components such as lactoferrin, lysozyme and secretory IgA considerably better than Holder pasteurization. We describe the inactivation of cytomegalovirus, a virus commonly excreted into breast milk, using UV-C irradiation. Full replication was ablated by various treatment doses. However, evidence of viral ...


Confirmation Of Emx2 Protein Binding Partners, Cody Gillman 2016 Central Washington University

Confirmation Of Emx2 Protein Binding Partners, Cody Gillman

All Master's Theses

The neocortex is a structure within mammalian brains that processes sensory input from eyes, ears, and touch receptors and mediates the conscious use of skeletal muscles. The processing of information related to each of these types of functions is localized within discrete areas of the neocortex, which are separated by sharp borders. Proper development of these functional areas is regulated during embryogenesis by several transcription factors that are expressed in distinct gradients across the progenitor layer of the neocortex, the ventricular zone. Despite the vast amount of progress that has been made in describing how these transcription factors impact the ...


Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), Elizabeth C. Craig, Brian S. Dorr, Katie C. Hanson-Dorr, Jed P. Sparks, Paul D. Curtis 2015 Cornell University

Isotopic Discrimination In The Double-Crested Cormorant (Phalacrocorax Auritus), Elizabeth C. Craig, Brian S. Dorr, Katie C. Hanson-Dorr, Jed P. Sparks, Paul D. Curtis

Brian S Dorr

The diet-tissue discrimination factor is the amount by which a consumer’s tissue varies isotopically from its diet, and is therefore a key element in models that use stable isotopes to estimate diet composition. In this study we measured discrimination factors in blood (whole blood, red blood cells and plasma), liver, muscle and feathers of Double- crested Cormorants (Phalacrocorax auritus) for stable isotope ratios of carbon, nitrogen and sulfur. Cormorants exhibited discrimination factors that differed significantly among tissue types (for carbon and nitrogen), and differed substantially (in the context of the isotopic variation among relevant prey species) from those observed ...


Elucidating The Role Of Hausp Ubiquitin Like Domains In The Catalytic Function Of Usp7, Anuj Patel, Nicole Davis, Andrew Mesecar 2015 Purdue University

Elucidating The Role Of Hausp Ubiquitin Like Domains In The Catalytic Function Of Usp7, Anuj Patel, Nicole Davis, Andrew Mesecar

The Summer Undergraduate Research Fellowship (SURF) Symposium

Ubiquitin specific proteases (USPs) are a class of enzymes involved in myriad cellular processes. One USP of great interest due to its oncogenic properties is USP7. In normal conditions USP7 is closely regulated due to its responsibility for destabilizing the tumor suppressor, p53, through the deubiquitination of MDM2. In multiple myeloma cases, it appears the regulation of USP7 subsides, as it is largely overexpressed, leading to the inappropriate degradation of p53. Inhibition of USP7 could, therefore, prove a viable target for cancer therapy. A greater understanding of USP7’s function and structure can lead to more insight into how this ...


Statistical Biophysics Blog: More Is Better: The Trajectory Ensemble Picture, Daniel M. Zuckerman 2015 Oregon Health & Science University

Statistical Biophysics Blog: More Is Better: The Trajectory Ensemble Picture, Daniel M. Zuckerman

Scholar Archive

The trajectory ensemble is fundamental in statistical physics and relatively easy to understand. It is also information-rich, as both equilibrium and non-equilibrium observables may be derived from it.


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