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Effect Of Turmeric On The Promoter Activity Of The Cyp6a8 Gene Of Drosophila Melanogaster, Alexa Stroh 2019 University of Tennessee, Knoxville

Effect Of Turmeric On The Promoter Activity Of The Cyp6a8 Gene Of Drosophila Melanogaster, Alexa Stroh

University of Tennessee Honors Thesis Projects

No abstract provided.


Characterization Of Psychromonas Aquimarina, A New Model Organism For Climate Change, Carrie Carpenter 2019 Harrisburg University of Science and Technology

Characterization Of Psychromonas Aquimarina, A New Model Organism For Climate Change, Carrie Carpenter

Experiential Learning Projects

The current increase of average global temperature puts 25 to 35 percent of plant and animal species at an increased risk of extinction (Climate Change, 2018). Changing any environmental factor, such as increasing growth temperature, can significantly impact any organisms’ ability to survive. Because of the diversity of organisms on the planet, it is not feasible to study how each individually might adapt, but rather it is more efficient to study select organisms. This research focuses on a psychrophilic bacterium, Psychromonas aquimarina, which can survive in colder regions where most bacteria would not. This bacterium was chosen because climate change ...


Ultrafine Carbon Nanoparticles Activate Inflammasome Signaling And Cell Death In Murine Macrophages, Alexander Soloniuk, Hadley Lamascus, Jay Brewster, John Mann 2019 Pepperdine University

Ultrafine Carbon Nanoparticles Activate Inflammasome Signaling And Cell Death In Murine Macrophages, Alexander Soloniuk, Hadley Lamascus, Jay Brewster, John Mann

Seaver College Research And Scholarly Achievement Symposium

Carbon black (CB) is the primary nanoparticulate component of air pollution from fossil fuel combustion. This work examines the cellular impact of ultrafine carbon (carbon black, CB) nanoparticles, that range in size down to 30 nm, upon murine macrophages. The size analysis of the carbon black nanoparticles was performed using atomic force microscopy (AFM) and transmission electron microscopy (TEM) techniques. RAW246.7 macrophage cells were exposed to CB doses ranging from 50 – 200 ug/ml in complete media. Analysis of cell survival over time revealed elevated rates of significant nuclear degradation and cell lifting after 48 hours of exposure, and ...


Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder 2019 Graz University of Technology

Promoter Library Designed For Fine-Tuned Gene Expression In Pichia Pastoris, Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoff P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James Cregg, Anton Glieder

Joan Lin-Cereghino

Although frequently used as protein production host, there is only a limited set of promoters available to drive the expression of recombinant proteins in Pichia pastoris. Fine-tuning of gene expression is often needed to maximize product yield and quality. However, for efficient knowledge-based engineering, a better understanding of promoter function is indispensable. Consequently, we created a promoter library by deletion and duplication of putative transcription factor-binding sites within the AOX1 promoter (PAOX1) sequence. This first library initially spanned an activity range between ∼6% and >160% of the wild-type promoter activity. After characterization of the promoter library employing a green ...


Condensed Protocol For Competent Cell Preparation And Transformation Of The Methylotrophic Yeast Pichia Pastoris, Joan Lin-Cereghino, William Wong, See Xiong, William Giang, Linda Luong, Jane Vu, Sabrina Johnson, Geoff P. Lin-Cereghino 2019 University of the Pacific

Condensed Protocol For Competent Cell Preparation And Transformation Of The Methylotrophic Yeast Pichia Pastoris, Joan Lin-Cereghino, William Wong, See Xiong, William Giang, Linda Luong, Jane Vu, Sabrina Johnson, Geoff P. Lin-Cereghino

Joan Lin-Cereghino

No abstract provided.


Endosome To Golgi Retrieval Of The Vacuolar Protein Sorting Receptor, Vps10p, Requires The Function Of The Vps29, Vps30, And Vps35 Gene Products, Matthew N. J. Seaman, Eric G. Marcusson, Joan Lin-Cereghino, Scott D. Emr 2019 University of California, San Diego

Endosome To Golgi Retrieval Of The Vacuolar Protein Sorting Receptor, Vps10p, Requires The Function Of The Vps29, Vps30, And Vps35 Gene Products, Matthew N. J. Seaman, Eric G. Marcusson, Joan Lin-Cereghino, Scott D. Emr

Joan Lin-Cereghino

Mutations in the S. cerevisiae VPS29 and VPS30 genes lead to a selective protein sorting defect in which the vacuolar protein carboxypeptidase Y (CPY) is missorted and secreted from the cell, while other soluble vacuolar hydrolases like proteinase A (PrA) are delivered to the vacuole. This phenotype is similar to that seen in cells with mutations in the previously characterized VPS10 and VPS35 genes. Vps10p is a late Golgi transmembrane protein that acts as the sorting receptor for soluble vacuolar hydrolases like CPY and PrA, while Vps35p is a peripheral membrane protein which cofractionates with membranes enriched in Vps10p. The ...


Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo 2019 Università di Torino

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo

Jared L. Anderson

Background

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

Results

In the present study, a MIL-based magnet-assisted dispersive liquid–liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal ...


An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald 2019 University of Massachusetts Medical School

An Automated Bayesian Pipeline For Rapid Analysis Of Single-Molecule Binding Data, Carlas Smith, Karina Jouravleva, Maximiliaan Huisman, Samson M. Jolly, Phillip D. Zamore, David Grünwald

David Grünwald

Single-molecule binding assays enable the study of how molecular machines assemble and function. Current algorithms can identify and locate individual molecules, but require tedious manual validation of each spot. Moreover, no solution for high-throughput analysis of single-molecule binding data exists. Here, we describe an automated pipeline to analyze single-molecule data over a wide range of experimental conditions. In addition, our method enables state estimation on multivariate Gaussian signals. We validate our approach using simulated data, and benchmark the pipeline by measuring the binding properties of the well-studied, DNA-guided DNA endonuclease, TtAgo, an Argonaute protein from the Eubacterium Thermus thermophilus. We ...


Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo 2019 Università di Torino

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo

Chemistry Publications

Background

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

Results

In the present study, a MIL-based magnet-assisted dispersive liquid–liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal ...


The Cytoplasmic Tail Domain Of The Vacuolar Protein Sorting Receptor Vps10p And A Subset Of Vps Gene Products Regulate Receptor Stability, Function, And Localization, Joan Lin-Cereghino, Eric G. Marcusson, Scott D. Emr 2019 University of California, San Diego

The Cytoplasmic Tail Domain Of The Vacuolar Protein Sorting Receptor Vps10p And A Subset Of Vps Gene Products Regulate Receptor Stability, Function, And Localization, Joan Lin-Cereghino, Eric G. Marcusson, Scott D. Emr

Joan Lin-Cereghino

VPS10 of Saccharomyces cerevisiae encodes a type I transmembrane receptor protein required for the sorting of the soluble vacuolar hydrolase carboxypeptidase Y (CPY). To characterize the essential structural features and intercompartmental transport itinerary of the CPY receptor, we have constructed mutant forms of Vps10p that alter the carboxyterminal cytoplasmic tail of the protein. In addition, we have analyzed the effect these mutations as well as mutations in several VPS genes have on the function, stability, and localization of Vps10p. Although wild-type Vps10p is very stable over a 3-h chase period, overproduction of Vps10p results in PEP4-dependent degradation of the receptor ...


Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. McIntosh, Eptisam Lambo, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson 2019 Dominican University of California

Scale Up Isolation Of Aaptamine For In Vivo Evaluation Indicates Its Neurobiological Activity Is Linked To The Delta Opioid Receptor, Nicole L. Mcintosh, Eptisam Lambo, Laura Millan-Lobo, Fei Li, Li He, Phillip Crews, Jennifer L. Whistler, Tyler Johnson

Tyler Johnson

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. The Mu, Delta, and Kappa (MOP, DOP, KOP) opioid receptors are particularly intriguing members of this receptor family as they are the targets involved in many neurobiological diseases such as addiction, pain, stress, anxiety, and depression. Recently we discovered that the aaptamine class of marine sponge derived natural products exhibit selective agonist activity in vitro for the DOP versus MOP receptor. Our findings may explain ...


Development And Validation Of A Rapid Method For The Detection Of Latrunculol A In Plasma., Jiajiu Shaw, Frederick A. Valeriote, Joseph Media, Tyler A. Johnson, Taro Amagata, Karen Tenney, Phillip Crews 2019 Henry Ford Health System, Detroit, Michigan, USA

Development And Validation Of A Rapid Method For The Detection Of Latrunculol A In Plasma., Jiajiu Shaw, Frederick A. Valeriote, Joseph Media, Tyler A. Johnson, Taro Amagata, Karen Tenney, Phillip Crews

Tyler Johnson

Latrunculol A is a recently discovered 6,7-dihydroxy analog of the potent actin inhibitor latrunculin A. Latrunculol A has exhibited greater cytotoxicity than latrunculin A against both murine and human colon tumor cell lines in vitro. Currently, there are no reports regarding the bioavailability of latrunculol A in vivo. This study was undertaken as a prelude to pharmacokinetic assessments and it is the first work where bioavailability of latrunculol A was studied. In the present work, a simple plasma preparation and a rapid HPLC method have been developed. Mouse plasma containing latrunculol A was first treated by acetonitrile and then ...


Defining The Biological Role Of The Connexin43 Carboxyl Terminal Helical Domains, Andrew Pham 2019 University of Nebraska at Omaha

Defining The Biological Role Of The Connexin43 Carboxyl Terminal Helical Domains, Andrew Pham

Student Research and Creative Activity Fair

Gap junctions play a vital role in cell to cell intercellular communication. Gap junctions are made of proteins called connexins with connexin43 (Cx43) being the most commonly studied isoform. Post-translational modifications of its carboxyl-terminal (CT) tail regulate the gating and degradation of gap junction channels. Casein kinase I (CK1) phosphorylates residues in between two alpha helical domains (A315 - M320 and D340 - A348) on the CT tail, opening gap junction channels. These two alpha helical domains have been found to dimerize. CK1 phosphorylation is necessary for opening gap junction channels and we hypothesize that this phosphorylation inhibits the dimerization of these ...


Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid 2019 University of Nebraska at Omaha

Targeted Therapy For The Future: The Use Of Novel Antimicrobial Peptides Against P. Aeurginosa, Matthew Froid

Student Research and Creative Activity Fair

Pathogenic bacteria, such as the gram-negative bacterium Pseudomonas aeruginosa, are becoming resistant to our current arsenal of antibiotics at an alarming rate. P. aeruginosa is a leading cause of nosocomial acquired infections and is a primary co-morbidity in patients with compromised immune systems. One potential source of new antibiotic agents is antimicrobial peptides. Antimicrobial peptides (AMPs) are small proteins, and some have shown a high degree of efficacy and broad-spectrum activity against both Gram-positive and Gram-negative bacteria. An experimental AMP that has been developed by Dr. Wang at UNMC, DASamp2, has shown to be effective against virulent bacteria, including P ...


Gene Ap2iii-3 Affects Stage Conversion In Toxoplasma Gondii, LeeAnna Lui 2019 University of Nebraska at Omaha

Gene Ap2iii-3 Affects Stage Conversion In Toxoplasma Gondii, Leeanna Lui

Student Research and Creative Activity Fair

Toxoplasma gondii is an intracellular parasite that infects roughly 1/3 of the world’s population. T. gondii has primarily two stages in its life cycle: the tachyzoite and bradyzoite stage. In its tachyzoite stage, T. gondii replicates and infects quickly in its host cells. However, after a few weeks, due to the pressure of the host’s immune system, T. gondii transforms in a chronic, slow replicating stage, where it forms cysts inside of its host. The initiation of the bradyzoite induction is dependent on a set of early genes. Through microarray analysis and other computational assays, a subset ...


Data Analytics Pipeline For Rna Structure Analysis Via Shape, Quinn Nelson 2019 University of Nebraska at Omaha

Data Analytics Pipeline For Rna Structure Analysis Via Shape, Quinn Nelson

Student Research and Creative Activity Fair

Coxsackievirus B3 (CVB3) is a cardiovirulent enterovirus from the family Picornaviridae. The RNA genome houses an internal ribosome entry site (IRES) in the 5’ untranslated region (5’UTR) that enables cap-independent translation. Ample evidence suggests that the structure of the 5’UTR is a critical element for virulence. We probe RNA structure in solution using base-specific modifying agents such as dimethyl sulfate as well as backbone targeting agents such as N-methylisatoic anhydride used in Selective 2’-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE). We have developed a pipeline that merges and evaluates base-specific and SHAPE data together with statistical analyses ...


Large Scale Dynamical Model Of Macrophage/Hiv Interactions, Matthew M. Froid 2019 University of Nebraska at Omaha

Large Scale Dynamical Model Of Macrophage/Hiv Interactions, Matthew M. Froid

Student Research and Creative Activity Fair

Properties emerge from the dynamics of large-scale molecular networks that are not discernible at the individual gene or protein level. Mathematical models - such as probabilistic Boolean networks - of molecular systems offer a deeper insight into how these emergent properties arise. Here, we introduce a non-linear, deterministic Boolean model of protein, gene, and chemical interactions in human macrophage cells during HIV infection. Our model is composed of 713 nodes with 1583 interactions between nodes and is responsive to 38 different inputs including signaling molecules, bacteria, viruses, and HIV viral particles. Additionally, the model accurately simulates the dynamics of over 50 different ...


The Value Of Universally Available Raw Nmr Data For Transparency, Reproducibility, And Integrity In Natural Product Research., James B McAlpine, Shao-Nong Chen, Andrei Kutateladze, John B MacMillan, Giovanni Appendino, Andersson Barison, Mehdi A Beniddir, Maique W Biavatti, Stefan Bluml, Asmaa Boufridi, Mark S Butler, Robert J Capon, Young H Choi, David Coppage, Phillip Crews, Michael T Crimmins, Marie Csete, Pradeep Dewapriya, Joseph M Egan, Mary J Garson, Grégory Genta-Jouve, William H Gerwick, Harald Gross, Mary Kay Harper, Precilia Hermanto, James M Hook, Luke Hunter, Damien Jeannerat, Nai-Yun Ji, Tyler A. Johnson, David G I Kingston, Hiroyuki Koshino, Hsiau-Wei Lee, Guy Lewin, Jie Li, Roger G Linington, Miaomiao Liu, Kerry L McPhail, Tadeusz F Molinski, Bradley S Moore, Joo-Won Nam, Ram P Neupane, Matthias Niemitz, Jean-Marc Nuzillard, Nicholas H Oberlies, Fernanda M M Ocampos, Guohui Pan, Ronald J Quinn, D Sai Reddy, Jean-Hugues Renault, José Rivera-Chávez, Wolfgang Robien, Carla M Saunders, Thomas J Schmidt, Christoph Seger, Ben Shen, Christoph Steinbeck, Hermann Stuppner, Sonja Sturm, Orazio Taglialatela-Scafati, Dean J Tantillo, Robert Verpoorte, Bin-Gui Wang, Craig M Williams, Philip G Williams, Julien Wist, Jian-Min Yue, Chen Zhang, Zhengren Xu, Charlotte Simmler, David C Lankin, Jonathan Bisson, Guido F Pauli 2019 University of Illinois at Chicago, Illinois, USA

The Value Of Universally Available Raw Nmr Data For Transparency, Reproducibility, And Integrity In Natural Product Research., James B Mcalpine, Shao-Nong Chen, Andrei Kutateladze, John B Macmillan, Giovanni Appendino, Andersson Barison, Mehdi A Beniddir, Maique W Biavatti, Stefan Bluml, Asmaa Boufridi, Mark S Butler, Robert J Capon, Young H Choi, David Coppage, Phillip Crews, Michael T Crimmins, Marie Csete, Pradeep Dewapriya, Joseph M Egan, Mary J Garson, Grégory Genta-Jouve, William H Gerwick, Harald Gross, Mary Kay Harper, Precilia Hermanto, James M Hook, Luke Hunter, Damien Jeannerat, Nai-Yun Ji, Tyler A. Johnson, David G I Kingston, Hiroyuki Koshino, Hsiau-Wei Lee, Guy Lewin, Jie Li, Roger G Linington, Miaomiao Liu, Kerry L Mcphail, Tadeusz F Molinski, Bradley S Moore, Joo-Won Nam, Ram P Neupane, Matthias Niemitz, Jean-Marc Nuzillard, Nicholas H Oberlies, Fernanda M M Ocampos, Guohui Pan, Ronald J Quinn, D Sai Reddy, Jean-Hugues Renault, José Rivera-Chávez, Wolfgang Robien, Carla M Saunders, Thomas J Schmidt, Christoph Seger, Ben Shen, Christoph Steinbeck, Hermann Stuppner, Sonja Sturm, Orazio Taglialatela-Scafati, Dean J Tantillo, Robert Verpoorte, Bin-Gui Wang, Craig M Williams, Philip G Williams, Julien Wist, Jian-Min Yue, Chen Zhang, Zhengren Xu, Charlotte Simmler, David C Lankin, Jonathan Bisson, Guido F Pauli

Tyler Johnson

With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data ...


The Potential Of Achiral Sponge-Derived And Synthetic Bromoindoles As Selective Cytotoxins Against Panc-1 Tumor Cells., Nicholas Lorig-Roach, Frances Hamkins-Indik, Tyler A. Johnson, Karen Tenney, Frederick A Valeriote, Phillip Crews 2019 University of California, Santa Cruz, California, USA

The Potential Of Achiral Sponge-Derived And Synthetic Bromoindoles As Selective Cytotoxins Against Panc-1 Tumor Cells., Nicholas Lorig-Roach, Frances Hamkins-Indik, Tyler A. Johnson, Karen Tenney, Frederick A Valeriote, Phillip Crews

Tyler Johnson

Our quest to isolate and characterize natural products with in vitro solid tumor selectivity is driven by access to repositories of Indo-Pacific sponge extracts. In this project an extract of a species of Haplosclerida sponge obtained from the US NCI Natural Products Repository displayed, by in vitro disk diffusion assay (DDA) and IC


Mass Stranding Of Marine Birds Caused By A Surfactant-Producing Red Tide., David A. Jessup, Melissa A. Miller, John P. Ryan, Hannah M Nevins, Heather A. Kerkering, Abdou Mekebri, David B. Crane, Tyler A. Johnson, Raphael M. Kudela 2019 California Department of Fish and Game, Marine Wildlife Veterinary Care and Research Center, California, USA

Mass Stranding Of Marine Birds Caused By A Surfactant-Producing Red Tide., David A. Jessup, Melissa A. Miller, John P. Ryan, Hannah M Nevins, Heather A. Kerkering, Abdou Mekebri, David B. Crane, Tyler A. Johnson, Raphael M. Kudela

Tyler Johnson

In November-December 2007 a widespread seabird mortality event occurred in Monterey Bay, California, USA, coincident with a massive red tide caused by the dinoflagellate Akashiwo sanguinea. Affected birds had a slimy yellow-green material on their feathers, which were saturated with water, and they were severely hypothermic. We determined that foam containing surfactant-like proteins, derived from organic matter of the red tide, coated their feathers and neutralized natural water repellency and insulation. No evidence of exposure to petroleum or other oils or biotoxins were found. This is the first documented case of its kind, but previous similar events may have gone ...


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