Biochemistry, Biophysics, and Structural Biology Commons^™

Model File Name: Ssdna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssDNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of DNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssDNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Nucleosome.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Nucleosome.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a crude representation of a nucleosome intended to accompany the H1 histone protein and a long, thin double stranded DNA helix model in order to illustrate DNA packaging and supercoiling. This model is designed to go with a teaching module on DNA supercoiling. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Nucleosome”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible …

Model File Name: Tf-Monomer-Stick.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: TF-monomer-stick.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). This model is designed to go with a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF monomer”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Strong & Flexible Plastic material.

Model File Name: Rna-Short-Helix.X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: RNA-short-helix.x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a DNA helix in which the atoms are colored by heteroatom (PDB: 1lmb). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “RNA helix - polynucleotide molecule”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full Color Sandstone material.

Video Guide To Design Flexible Dna.Mp4, Michelle Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian Couch, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Video guide to design flexible DNA.mp4

Authors: Michelle E Howell, Karin van Dijk, Christine S Booth, Tomas Helikar, Brian A Couch, Rebecca L Roston

This 30-minute video includes step-by-step instructions to design and 3-D print a long flexible DNA model that mimics the structure and function of DNA. The instructions are applicable for designing the model using open-source 3-D computer graphics software Blender 2.79 which is available for download at https://www.blender.org/download/.

.mp4 file download (70 MB) below.

Model File Name: Ssrna.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: ssRNA.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a single stranded piece of RNA in stick representation (PDB: 1ehz). This model is designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “ssRNA”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the Elasto Plastic material.

Model File Name: Helix_H2o_Sphere2.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: Helix_H2O_sphere2.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a space fill representation of a protein α-helix (PDB: 3vjo). A space fill water molecule is also represented to illustrate the lack of space down the axis of an α-helix. This model can accompany a corresponding stick representation, a kinked α-helix, and a β-sheet. This model is designed to accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Helix and Water (Space-fill) …

Model File Name: Beta-Sheet_Rod 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: beta-sheet_rod 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein β-sheet (PDB: 3vjo). This model is designed to accompany three other α-helix models: a space-fill representation of a straight α-helix, a stick representation of a straight α-helix, and a stick representation of a kinked α-helix. These models accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Beta-sheet_Thick”. This model has been printed successfully using …

Model File Name: Alpha Helix Pro-Gly 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: alpha helix pro-gly 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein α-helix with proline and glycine residues highlighted (PDB: 3vjo). This model is designed to accompany a straight α-helix in space fill representation, a straight α-helix in stick representation, and a stick β-sheet model as well as a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Alpha Helix_Pro-Gly”. This model has been printed successfully using these parameters …

Model File Name: Alpha Helix 0.7.Dae, Michelle Howell, Rebecca Roston

3-D Printed Model Structural Files

Model file name: alpha helix 0.7.dae

Authors: Michelle E Howell, Rebecca L Roston

This is a teaching model of a stick representation of a protein α-helix (PDB: 3vjo). This model can accompany a corresponding space fill representation, a kinked α-helix, and a β-sheet. These models were designed to accompany a teaching module illustrating protein secondary structure and function. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Alpha Helix_Thick”. This model has been printed successfully using these parameters on Shapeways’ binder jetting printer in the Coated Full Color …

Effects Of Lipid Activating Chemical Compounds On The Growth And Production Of Fatty Acids And Metabolites In Green Algae, David Nguyen, Nishikant Wase, Concetta Dirusso

UCARE: Research Products

This study examines the effects of small molecule lipid activating chemical compound, discovered from the high throughput screening (HTS) (2) methods of previous FATTT Lab studies on the growth and production of lipids and metabolites in microalgae. For this study, the effects of two lipid inducing chemical compounds from the HTS method were implemented with the microalgae strain Chlamydomonas reinhardtii CC-125. This experiment focused on scaling up to large amounts of culture, approximately 1L. These cultures were grown in specially designed large bioreactors that were able to accommodate for such large volume of algal culture. Algal cells were treated with …

Characterization Of Metabolic Network In T-Helper 2 Cells, Bailee Lichter

UCARE: Research Products

T-helper 2 (Th2) cells function in the adaptive immune system to coordinate responses to large extracellular pathogens (Luckheerham, 2012). Th2 cells are one of the differentiated subtypes cells of CD4+ T cells. CD4+ T cells recognize foreign pathogens and differenitated in specialized subtypes to affectively destroy the pathogen (Luckheerham, 2012). Upon CD4+ T cell activation, the cells undergo metabolic reprogaming, resulting in a shift in metabolism (Almedia, 2016).

We have successfully created a Th2 metabolic network model. The Th2 metabolic network model contains 1151 genes, 2601 metabolites, and 4654 reactions.

Efficacy Of Oral Administration Of Sodium Iodide To Prevent Bovine Respiratory Disease Complex, B. M. Shoemake, B. L. Vander Ley, B. W. Newcomer, M. C. Heller

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: The prevention of bovine respiratory disease complex (BRD) in beef cattle is important to maintaining health and productivity of calves in feeding operations.

Objective: Determine whether BRD bacterial and viral pathogens are susceptible to the lactoperoxidase/hydrogen peroxide/ iodide (LPO/H₂O₂/I^-) system in vitro and to determine whether the oral administration of sodium iodide (NaI) could achieve sufficient concentrations of iodine (I) in the respiratory secretions of weaned beef calves to inactivate these pathogens in vivo.

Animals: Sixteen weaned, apparently healthy, commercial beef calves from the University of Missouri, College of Veterinary Medicine teaching herd. …

Photosystem Ii Subunit S Overexpression Increases The Efficiency Of Water Use In A Field-Grown Crop, Katarzyna Glowacka, Johannes Kromdijk, Katherine Kucera, Jiayang Xie, Amanda P. Cavanagh, Lauriebeth Leonelli, Andrew D. B. Leakey, Donald R. Ort, Krishna K. Niyogi, Stephen P. Long

Department of Biochemistry: Faculty Publications

Insufficient water availability for crop production is a mounting barrier to achieving the 70% increase in food production that will be needed by 2050. One solution is to develop crops that require less water per unit mass of production. Water vapor transpires from leaves through stomata, which also facilitate the influx of CO2 during photosynthetic assimilation. Here, we hypothesize that Photosystem II Subunit S (PsbS) expression affects a chloroplastderived signal for stomatal opening in response to light, which can be used to improve wateruse efficiency. Transgenic tobacco plants with a range of PsbS expression, from undetectable to 3.7 …

Simulation Of Stimulation: Cytokine Dosage And Cell Cycle Crosstalk Driving Timing-Dependent T Cell Differentiation, Matteo Barberis, Tomáš Helikar, Paul Verbruggen

Department of Biochemistry: Faculty Publications

Triggering an appropriate protective response against invading agents is crucial to the effectiveness of human innate and adaptive immunity. Pathogen recognition and elimination requires integration of a myriad of signals from many different immune cells. For example, T cell functioning is not qualitatively, but quantitatively determined by cellular and humoral signals. Tipping the balance of signals, such that one of these is favored or gains advantage on another one, may impact the plasticity of T cells. This may lead to switching their phenotypes and, ultimately, modulating the balance between proliferating and memory T cells to sustain an appropriate immune response. …

Computational Systems Biology Approach For The Study Of Rheumatoid Arthritis: From A Molecular Map To A Dynamical Model, Vidisha Singh, Marek Ostaszewski, George D. Kalliolias, Gilles Chiocchia, Robert Olaso, Elisabeth Petit-Teixeira, Tomáš Helikar, Anna Niarakis

Department of Biochemistry: Faculty Publications

In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA). We are constructing a detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts’ advice. The RA map will be web-published in the coming months in the form of an interactive map, using the MINERVA platform, allowing for easy access, navigation and search of all molecular pathways implicated in RA, serving thus, as an on line knowledgebase for the disease. Moreover the map could be used as a template for Omics data …

The Colomoto Interactive Notebook: Accessible And Reproducible Computational Analyses For Qualitative Biological Networks, Aurelien Naldi, Celine Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loic Pauleve

Department of Biochemistry: Faculty Publications

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together,many times with additional manual steps. The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users’ learning curve of these technologies. The framework …

A Mechanistic Computational Model Reveals That Plasticity Of Cd4+ T Cell Differentiation Is A Function Of Cytokine Composition And Dosage, Bhanwar Lal Puniya, Robert G. Todd, Akram Mohammed, Deborah M. Brown, Matteo Barberis, Tomáš Helikar

Department of Biochemistry: Faculty Publications

CD4+ T cells provide cell-mediated immunity in response to various antigens. During an immune response, naïve CD4+ T cells differentiate into specialized effector T helper (Th1, Th2, and Th17) cells and induced regulatory (iTreg) cells based on a cytokine milieu. In recent studies, complex phenotypes resembling more than one classical T cell lineage have been experimentally observed. Herein, we sought to characterize the capacity of T cell differentiation in response to the complex extracellular environment. We constructed a comprehensive mechanistic (logical) computational model of the signal transduction that regulates T cell differentiation. The model’s dynamics were characterized and analyzed under …

Reactive Oxygen Species In Chronic Obstructive Pulmonary Disease, Samia Boukhenouna, Mark A. Wilson, Karim Bahmed, Beata Kosmider

Department of Biochemistry: Faculty Publications

Chronic obstructive pulmonary disease (COPD) includes chronic bronchitis and emphysema. Environmental exposure, primarily cigarette smoking, can cause high oxidative stress and is the main factor of COPD development. Cigarette smoke also contributes to the imbalance of oxidant/antioxidant due to exogenous reactive oxygen species (ROS). Moreover, endogenously released ROS during the inflammatory process and mitochondrial dysfunction may contribute to this disease progression. ROS and reactive nitrogen species (RNS) can oxidize different biomolecules such as DNA, proteins, and lipids leading to epithelial cell injury and death. Various detoxifying enzymes and antioxidant defense systems can be involved in ROS removal. In this review, …

Complete Genome Sequence Of Moraxella Bovis Strain Epp-63 (300), An Etiologic Agent Of Infectious Bovine Keratoconjunctivitis, John Dustin Loy, Aaron M. Dickey, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

We report here the complete closed genome sequence of Moraxella bovis strain Epp-63 (300) (Epp63). This strain was isolated from an infectious bovine keratoconjunctivitis (IBK) case in 1963. Since then, Epp63 has been used extensively for IBK research. Consequently, the genome sequence of Epp63 should help elucidate IBK host-pathogen interactions.

Development Of Septic Polysynovitis And Uveitis In Foals Experimentally Infected With Rhodococcus Equi, Laura Huber, Steeve Giguère, Londa J. Berghaus, Amanda Hanafi, Sarah Vitosh-Sillman, Sarah L. Czerwinski

School of Veterinary and Biomedical Sciences: Faculty Publications

Rhodococcus equi is one of the most important causes of disease in foals. Infection is typically characterized by pyogranulomatous pneumonia although extrapulmonary infections occur occasionally. Uveitis and polysynovitis have been reported in foals naturally infected with R. equi and are thought to be the result of an immune-mediated process. However, the pathogenesis of these conditions is poorly understood. The objectives of this study were to document the occurrence of uveitis and polysynovitis after experimental infection with R. equi and to determine if these disorders are the direct result of infection at these sites. Foals between 3 and 4 weeks of …

Alkaline Stabilization Of Manure Slurry Inactivates Porcine Epidemic Diarrhea Virus, Erin E. Stevens, Daniel N. Miller, Bethany A. Brittenham, Sarah J. Vitosh-Sillman, Bruce W. Brodersen, Virginia L. Jin, John D. Loy, Amy M. Schmidt

School of Veterinary and Biomedical Sciences: Faculty Publications

Hydrated lime manure treatment was evaluated to determine porcine epidemic diarrhea virus (PEDV) susceptibility to alkaline stabilization. At pH 10, PEDV decreased (quantitative polymerase chain reaction) and lost infectivity (swine bioassay). Although ammonium decreased above pH 9 (up to 25%), alkaline stabilization managed to control potential infection from manure sources.

Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry Identification Of Moraxella Bovoculi And Moraxella Bovis Isolates From Cattle, Kara Robbins, Aaron M. Dickey, Michael L. Clawson, John Dustin Loy

School of Veterinary and Biomedical Sciences: Faculty Publications

Infectious bovine keratoconjunctivitis (IBK) is an economically significant disease caused by Moraxella bovis. Moraxella bovoculi, although not reported to cause IBK, has been isolated from the eyes of cattle diagnosed with IBK. Identification of M. bovis and M. bovoculi can be performed using biochemical or DNA-based approaches, both of which may be time consuming and inconsistent between laboratories. We conducted a comparative evaluation of M. bovoculi and M. bovis identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with a database provided by Bruker Daltonics (termed the BDAL database), the BDAL database supplemented with spectra generated in …

Circadian Behavioral Responses To Light And Optic Chiasm-Evoked Glutamatergic Epscs In The Suprachiasmatic Nucleus Of Iprgc Conditional Vglut2 Knock-Out Mice, Michael G. Moldavan, Patricia J. Sollars, Michael R. Lasarev, Charles N. Allen, Gary E. Pickard

School of Veterinary and Biomedical Sciences: Faculty Publications

Intrinsically photosensitive retinal ganglion cells (ipRGCs) innervate the hypothalamic suprachiasmatic nucleus (SCN), a circadian oscillator that functions as a biological clock. ipRGCs use vesicular glutamate transporter 2 (vGlut2) to package glutamate into synaptic vesicles and light-evoked resetting of the SCN circadian clock is widely attributed to ipRGC glutamatergic neurotransmission. Pituitary adenylate cyclase-activating polypeptide (PACAP) is also packaged into vesicles in ipRGCs and PACAP may be coreleased with glutamate in the SCN. vGlut2 has been conditionally deleted in ipRGCs in mice [conditional knock-outs (cKOs)] and their aberrant photoentrainment and residual attenuated light responses have been ascribed to ipRGC PACAP release. However, …

Development Of A Multiplex Real-Time Pcr Assay Using Two Thermocycling Platforms For Detection Of Major Bacterial Pathogens Associated With Bovine Respiratory Disease Complex From Clinical Samples, John Dustin Loy, Laura Leger, Aspen M. Workman, Michael L. Clawson, Ece Bulut, Bing Wang

School of Veterinary and Biomedical Sciences: Faculty Publications

Bovine respiratory disease complex (BRDC) is one of the most significant diseases of cattle. Bacterial pathogens involved in BRDC include Mannheimia haemolytica, Mycoplasma bovis, Histophilus somni, and Pasteurella multocida. We developed and evaluated a multiplexed real-time hydrolysis probe (rtPCR) assay using block-based Peltier and rotary-based thermocycling on lung tissue, nasal swabs, and deep nasopharyngeal swabs. The rtPCR results were compared to culture or a gel-based M. bovis PCR using statistical analysis to determine optimum quantification cycle (Cq) cutoffs to maximize agreement. The limits of detection were 1.2–12 CFU/reaction for each pathogen. M. haemolytica was the most prevalent organism detected …

Coordinated Regulation Of Transcription By Ccpa And The Staphylococcus Aureus Twocomponent System Hptrs, Joseph M. Reed, Sean Olson, Danielle F. Brees, Caitlin E. Griffin, Ryan A. Grove, Paul J. Davis, Stephen D. Kachman, Jiri Adamec, Greg A. Somerville

School of Veterinary and Biomedical Sciences: Faculty Publications

The success of Staphylococcus aureus as a pathogen is due in part to its ability to adapt to changing environmental conditions using signal transduction pathways, such as metaboliteresponsive regulators and two-component systems. S. aureus has a two-component system encoded by the gene pair sav0224 (hptS) and sav0223 (hptR) that regulate the hexose phosphate transport (uhpT) system in response to extracellular glucose-6-phosphate. Glycolytic intermediates such as glucose-6-phosphate are important carbon sources that also modulate the activity of the global metabolite-responsive transcriptional regulator CcpA. Because uhpT has a putative CcpA binding site in its promoter and …

Novel Docosahexaenoic Acid Ester Of Phloridzin Inhibits Proliferation And Triggers Apoptosis In An In Vitro Model Of Skin Cancer, Theodora Mantso, Dimitrios T. Trafalis, Sotiris Botaitis, Rodrigo Franco, Aglaia Pappa, H. P. Vasantha Rupasinghe, Mihalis I. Panayiotidis

School of Veterinary and Biomedical Sciences: Faculty Publications

Skin cancer is among the most common cancer types accompanied by rapidly increasing incidence rates, thus making the development of more efficient therapeutic approaches a necessity. Recent studies have revealed the potential role of decosahexaenoic acid ester of phloridzin (PZDHA) in suppressing proliferation of liver, breast, and blood cancer cell lines. In the present study, we investigated the cytotoxic potential of PZDHA in an in vitro model of skin cancer consisting of melanoma (A375), epidermoid carcinoma (A431), and non-tumorigenic (HaCaT) cell lines. Decosahexaenoic acid ester of phloridzin led to increased cytotoxicity in all cell lines as revealed by cell viability …

Whole Genome Sequencing Of Moraxella Bovoculi Reveals High Genetic Diversity And Evidence For Interspecies Recombination At Multiple Loci, Aaron M. Dickey, Gennie Schuller, John D. Loy, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

Moraxella bovoculi is frequently cultured from the ocular secretions and conjunctiva of cattle with Infectious Bovine Keratoconjunctivitis (IBK). Previous work has shown that single nucleotide polymorphism (SNP) diversity in this species is quite high with 81,284 SNPs identified in eight genomes representing two distinct genotypes isolated from IBK affected eyes (genotype 1) and the nasopharynx of cattle without clinical IBK signs (genotype 2), respectively. The goals of this study were to identify SNPs from a collection of geographically diverse and epidemiologically unlinked M. bovoculi strains from the eyes of IBK positive cattle (n = 183) and another from the eyes …

Differential Modulation Of Human Gabac‑Ρ1 Receptor By Sulfur‑Containing Compounds Structurally Related To Taurine, Lenin David Ochoa‑De La Paz, Martin González‑Andrade, Herminia Pasantes‑Morales, Rodrigo Franco, Rubén Zamora‑Alvarado, Edgar Zenteno, Hugo Quiroz‑Mercado, Roberto Gonzales‑Salinas, Rosario Gulias‑Cañizo

School of Veterinary and Biomedical Sciences: Faculty Publications

Background: The amino acid taurine (2-Aminoethanesulfonic acid) modulates inhibitory neurotransmitter receptors. This study aimed to determine if the dual action of taurine on GABAC- ρ1R relates to its structure. To address this, we tested the ability of the structurally related compounds homotaurine, hypotaurine, and isethionic acid to modulate GABAC- ρ1R.

Results: In Xenopus laevis oocytes, hypotaurine and homotaurine partially activate heterologously expressed GABAC- ρ1R, showing an increment in its deactivation time with no changes in channel permeability, whereas isethionic acid showed no effect. Competitive assays suggest that hypotaurine and homotaurine compete for the GABA-binding site. In addition, their effects were …

Using Art And Story To Explore How Primary School Students In Rural Tanzania Understand Planetary Health: A Qualitative Analysis, Elizabeth Vanwormer, Jesca Mlawa, Elizabeth Komba, Christopher Gustafson, Hilda Mrema, Jenny M. Dauer

School of Veterinary and Biomedical Sciences: Faculty Publications

Background The global planetary health community increasingly recognises the need to prepare students to investigate and address connections between environmental change and human health. As we strive to support education on planetary health themes for students of all ages, understanding students’ concepts of linkages between the health of people and animals, and their shared environments might advance educational approaches. Children living in villages bordering Ruaha National Park in Iringa Region, Tanzania, have direct experience of these connections as they share a water-stressed but biodiverse environment with domestic animals and wildlife. Livelihoods in these villages depend predominantly on crop and livestock …