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Structure And Stability Of Recombinant Bovine Odorant-Binding Protein: Ii. Unfolding Of The Monomeric Forms, Olga V. Stepanenko, Denis O. Roginski, Olesya V. Stepanenko, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities of the recombinant bOBP and its monomeric variants, the bOBP-Gly121+ mutant containing an additional glycine residue after the residue 121 of the bOBP, and the GCC-bOBP mutant obtained from the bOBP-Gly121+ form by introduction of the Trp64Cys/His155Cys double mutation to restore the canonical disulfide bond. We also analyzed the effect of the natural ligand binding on the conformational stabilities of these bOBP …

Yersinia Pestis Caf1 Protein: Effect Of Sequence Polymorphism On Intrinsic Disorder Propensity, Serological Cross-Reactivity And Cross-Protectivity Of Isoforms, Pavel Kh. Kopylov, Mikhail E. Platonov, Vitaly G. Ablamunits, Tat’Yana I. Kombarova, Sergey A. Ivanov, Lidiya A. Kadnikova, Aleksey N. Somov, Svetlana V. Dentovskaya, Vladimir N. Uversky, Andrey P. Anisimov

Molecular Medicine Faculty Publications

Yersinia pestis Caf1 is a multifunctional protein responsible for antiphagocytic activity and is a key protective antigen. It is generally conserved between globally distributed Y. pestis strains, but Y. pestis subsp. microtus biovar caucasica strains circulating within populations of common voles in Georgia and Armenia were reported to carry a single substitution of alanine to serine. We investigated polymorphism of the Caf1 sequences among other Y. pestis subsp. microtus strains, which have a limited virulence in guinea pigs and in humans. Sequencing of caf1 genes from 119 Y. pestis strains belonging to different biovars within subsp. microtus showed that the …

Intrinsically Disordered Side Of The Zika Virus Proteome, Rajanish Giri, Deepak Kumar, Nitin Sharma, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Over the last few decades, concepts of protein intrinsic disorder have been implicated in different biological processes. Recent studies have suggested that intrinsically disordered proteins (IDPs) provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion in host cells. In case of Zika virus, the roles of protein intrinsic disorder in mechanisms of pathogenesis are not completely understood. In this study, we have analyzed the prevalence of intrinsic disorder in Zika virus proteome (strain MR 766). Our analyses revealed that Zika virus polyprotein is enriched with intrinsically disordered protein regions (IDPRs) and …

Structure And Stability Of Recombinant Bovine Odorant-Binding Protein: Ii. Unfolding Of The Monomeric Forms, Olga V. Stepanenko, Denis O. Roginskii, Olesya V. Stepanenko, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities of the recombinant bOBP and its monomeric variants, the bOBP-Gly121+ mutant containing an additional glycine residue after the residue 121 of the bOBP, and the GCC-bOBP mutant obtained from the bOBP-Gly121+ form by introduction of the Trp64Cys/His155Cys double mutation to restore the canonical disulfide bond. We also analyzed the effect of the natural ligand binding on the conformational stabilities of these bOBP …

Compartmentalization And Functionality Of Nuclear Disorder: Intrinsic Disorder And Protein-Protein Interactions In Intra-Nuclear Compartments, Fanchi Meng, Insung Na, Lukasz Kurgan, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The cell nucleus contains a number of membrane-less organelles or intra-nuclear compartments. These compartments are dynamic structures representing liquid-droplet phases which are only slightly denser than the bulk intra-nuclear fluid. They possess different functions, have diverse morphologies, and are typically composed of RNA (or, in some cases, DNA) and proteins. We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML) nuclear bodies, nuclear lamina, nuclear pores, and perinuclear compartment and compared them with ~29,863 non-nuclear proteins from mouse proteome. Our analysis revealed that intrinsic disorder is enriched in the …

Looking At The Carcinogenicity Of Human Insulin Analogues Via The Intrinsic Disorder Prism, Elrashdy M. Redwan, Moustafa H. Linjawi, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Therapeutic insulin, in its native and biosynthetic forms as well as several currently available insulin analogues, continues to be the protein of most interest to researchers. From the time of its discovery to the development of modern insulin analogues, this important therapeutic protein has passed through several stages and product generations. Beside the well-known link between diabetes and cancer risk, the currently used therapeutic insulin analogues raised serious concerns due to their potential roles in cancer initiation and/or progression. It is possible that structural variations in some of the insulin analogues are responsible for the appearance of new oncogenic species …

Dancing Protein Clouds: The Strange Biology And Chaotic Physics Of Intrinsically Disordered Proteins, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally …

Order, Disorder, And Everything In Between, Shelly Deforte, Vladimir N. Uversky

Molecular Medicine Faculty Publications

In addition to the “traditional” proteins characterized by the unique crystal-like structures needed for unique functions, it is increasingly recognized that many proteins or protein regions (collectively known as intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs)), being biologically active, do not have a specific 3D-structure in their unbound states under physiological conditions. There are also subtler categories of disorder, such as conditional (or dormant) disorder and partial disorder. Both the ability of a protein/region to fold into a well-ordered functional unit or to stay intrinsically disordered but functional are encoded in the amino acid sequence. Structurally, IDPs/IDPRs …

Expression, Purification, And Characterization Of Interleukin-11 Orthologues, Andrei S. Sokolov, Alexei S. Kazakov, Valery V. Solovyev, Ramis G. Ismailov, Vladimir N. Uversky, Yulia S. Lapteva, Roman V. Mikhailov, Ekaterina V. Pavlova, Iana O. Terletskaya, Ludmila V. Ermolina, Sergei E. Permyakov, Eugene A. Permyakov, Eugene A. Permyakov

Molecular Medicine Faculty Publications

Interleukin-11 (IL-11) is a multifunctional cytokine implicated in several normal and pathological processes. The decoding of IL-11 function and development of IL-11-targeted drugs dictate the use of laboratory animals and need of the better understanding of species specificity of IL-11 signaling. Here, we present a method for the recombinant interleukin-11 (rIL-11) production from the important model animals, mouse and macaque. The purified mouse and macaque rIL-11 interact with extracellular domain of human IL-11 receptor subunit α and activate STAT3 signaling in HEK293 cells co-expressing human IL-11 receptors with efficacies resembling those of human rIL-11. Hence, the evolutionary divergence does not …

Rnd3 As A Novel Target To Ameliorate Microvascular Leakage, Jerome W. Breslin, Dayle A. Daines, Travis M. Doggett, Kristine H. Kurtz, Flavia M. Souza-Smith, Xun E. Zhang, Mack H. Wu, Sarah Y. Yuan

Molecular Pharmacology & Physiology Faculty Publications

Background: Microvascular leakage of plasma proteins is a hallmark of inflammation that leads to tissue dysfunction. There are no current therapeutic strategies to reduce microvascular permeability. The purpose of this study was to identify the role of Rnd3, an atypical Rho family GTPase, in the control of endothelial barrier integrity. The potential therapeutic benefit of Rnd3 protein delivery to ameliorate microvascular leakage was also investigated.

Methods and Results: Using immunofluorescence microscopy, Rnd3 was observed primarily in cytoplasmic areas around the nuclei of human umbilical vein endothelial cells. Permeability to fluorescein isothiocyanate–albumin and transendothelial electrical resistance of human umbilical vein endothelial …

Island Building In The South China Sea: Detection Of Turbidity Plumes And Artificial Islands Using Landsat And Modis Data, Brian B. Barnes, Chuanmin Hu

Marine Science Faculty Publications

The South China Sea is currently in a state of intense geopolitical conflict, with six countries claiming sovereignty over some or all of the area. Recently, several countries have carried out island building projects in the Spratly Islands, converting portions of coral reefs into artificial islands. Aerial photography and high resolution satellites can capture snapshots of this construction, but such data are lacking in temporal resolution and spatial scope. In contrast, lower resolution satellite sensors with regular repeat sampling allow for more rigorous assessment and monitoring of changes to the reefs and surrounding areas. Using Landsat-8 data at ≥15-m resolution, …

Linking Oceanographic Modeling And Benthic Mapping With Habitat Suitability Models For Pink Shrimp On The West Florida Shelf, Peter J. Rubec, Jesse Lewis, David Reed, Christi Santi, Robert H. Weisberg, Lianyuan Zheng, Chris Jenkins, Charles F. Ashbaugh, Curt Lashley, Salvatore Versaggi

Marine Science Faculty Publications

Research was undertaken to model and map the spatial distributions and abundances of pink shrimp Farfantepenaeus duorarum on the West Florida Shelf (WFS) using habitat suitability modeling (HSM). Data loggers and electronic logbook systems on three shrimp boats were used to gather catch and effort data along with bottom temperature, salinity, and depth data at the fishing locations. Vessel monitoring system (VMS) data supplied by the fishing company helped delineate areas with high fishing activity. For the vessels participating in this study, significantly higher mean catch per unit effort (CPUE) of pink shrimp was realized on the WFS during June–September …

Recent Change - North Sea, Thomas Wahl

Marine Science Faculty Publications

This chapter discusses past and ongoing change in the following physical variables within the North Sea: temperature, salinity and stratification; currents and circulation; mean sea level; and extreme sea levels. Also considered are carbon dioxide; pH and nutrients; oxygen; suspended particulate matter and turbidity; coastal erosion, sedimentation and morphology; and sea ice. The distinctive character of the Wadden Sea is addressed, with a particular focus on nutrients and sediments. This chapter covers the past 200 years and focuses on the historical development of evidence (measurements, process understanding and models), the form, duration and accuracy of the evidence available, and what …

Satellite-Based Empirical Models Linking River Plume Dynamics With Hypoxic Area And Volume, Chengfeng Le, John C. Lehrter, Chuanmin Hu, Daniel R. Obenour

Marine Science Faculty Publications

Satellite-based empirical models explaining hypoxic area and volume variation were developed for the seasonally hypoxic (O₂ < 2 mg L⁻¹) northern Gulf of Mexico adjacent to the Mississippi River. Annual variations in midsummer hypoxic area and volume were related to Moderate Resolution Imaging Spectroradiometer-derived monthly estimates of river plume area (km²) and average, inner shelf chlorophyll a concentration (Chl a, mg m⁻³). River plume area in June was negatively related with midsummer hypoxic area (km²) and volume (km³), while July inner shelf Chl a was positively related to hypoxic area and volume. …

2016 Women's Soccer Media Guide, University Of South Florida. Athletic Communications Office, Lindsey Morrison, Erin Beck

Women's Soccer Media Guides

The media guide for the University of South Florida's (USF) 2016 women's soccer season. Included are sections on the 2016 season outlook, coaches and staff, player biographies, a 2015 season review, program records, program history, and USF Athletics media information. The team finished the season 12-4-3.

Dna Barcoding Reveals Mislabeling Of Game Meat Species On The U.S. Commercial Market, Charles Quinto, Rebecca Tinoco, Rosalee S. Hellberg

Food Science Faculty Articles and Research

Game meats represent a valuable specialty market in the United States that has high economic incentives associated with mislabeling. However, there is limited information on this topic. The purpose of this study was to conduct a market survey of game meats sold within the United States and identify instances of mislabeling using DNA barcoding. Products were also examined for the presence of threatened or endangered species. Fifty-four samples of whole-cut game meats were collected from online distributors in the United States and sequenced across a 658 base-pair region of the cytochrome c oxidase subunit I (COI) gene. The resulting DNA …

Identification Of Species In Ground Meat Products Sold On The U.S. Commercial Market Using Dna-Based Methods, Dawn Kane, Rosalee S. Hellberg

Food Science Faculty Articles and Research

The objective of this study was to test a variety of ground meat products sold on the U.S. commercial market for the presence of potential mislabeling. Forty-eight ground meat samples were purchased from online and retail sources, including both supermarkets and specialty meat retailers. DNA was extracted from each sample in duplicate and tested using DNA barcoding of the cytochrome c oxidase I (COI) gene. The resulting sequences were identified at the species level using the Barcode of Life Database (BOLD). Any samples that failed DNA barcoding went through repeat extraction and sequencing, and due to the possibility of a …

Afterword: Gesamtkunstwerk As Epistemic Space, Kevin S. Amidon Ph.D.

Modern Languages Faculty Publications

For two centuries, Gesamtkunstwerk—the ideal of the “total work of art”—has exerted a powerful influence over artistic discourse and practice, spurring new forms of collaboration and provoking debates over the political instrumentalization of art. Despite its popular conflation with the work of Richard Wagner, Gesamtkunstwerk’s lineage and legacies extend well beyond German Romanticism, as this wide-ranging collection demonstrates. In eleven compact chapters, scholars from a variety of disciplines trace the idea’s evolution in German-speaking Europe, from its foundations in the early nineteenth century to its manifold articulations and reimaginings in the twentieth century and beyond, providing an uncommonly broad perspective …

Easing The Encumbered Subject: Security, Speculation, And Capitalist Subjectivity, Kevin S. Amidon Ph.D., Daniel Krier

Modern Languages Faculty Publications

Capitalisms’ Future: Alienation, Emancipation and Critique frames 21st century economic and social possibilities in a dialogue between two forms of critical social theory: Marx’s critique of political economy that analyzes capitalism and the critique of political psychology that analyzes authoritarianism. Contributions from social theorists in sociology, philosophy, and cultural studies are brought together to dissect and critique capitalist crises, left-liberalism, left-Thatcherism, resistance to risk-pooling, idealist philosophy, undemocratic social character, status wages and authoritarian spectacles. Throughout, Marx’s centrality to critical social theory is confirmed, both alone and in in powerful combination with Adorno, Durkheim, Dubois, Lacan, Veblen, Weber and others. This …

To Catch A Terrorist: The Improper Use Of Profiling In U.S. Post-9/11 Counterterrorism, Kamillia Crawford

Honors Undergraduate Theses

The attacks of September 11, 2001 (9/11) caused thousands of deaths, national and global panic, and immediate action by the federal government to protect the borders of the United States of America (USA) from terrorism. In response to these attacks, the United States (U.S.) government enacted laws for law enforcement agencies to protect against terrorist activities. Law enforcement agencies are effective in combating terrorism, but their measures contain a major flaw - the improper use of race in profiling to address national security and public safety concerns. Racial profiling is an ineffective measure for preventing terrorism. There are solutions to …

The Integration Of Mobile Technology To Lower The Risk Of Developing Cervical Cancer In Hiv Positive Women, Tugce Kinik

Dissertations, Master's Theses and Master's Reports

Cervical cancer is the most common cancer in HIV positive women in the world [1]. According to epidemiologists, HPV infection alone will not initiate cervical cancer [2]. In addition to high risk HPV types, smoking, long term hormonal contraceptive use, high parity, HIV/AIDS infection, sexual activity before 20 years of age, multiple sexual partners, exposure to sexually transmitted disease, and family history of cervical cancer are other reasons to turn an HPV infection to the cervical cancer [3]. With the increasing global population, cervical cancer cases are expected to increase 46% until 2030 [4]. Effective prevention and control efforts will …

Caring Minds, University Of Texas Health Science Center At Houston School Of Nursing

Caring Minds

No abstract provided.

Self-Powered Microfluidic Device For Rapid Assay Of Antiplatelet Drugs, Bincy Jose, Peter Mccluskey, Niamh Gilmartin, Martin Somers, Dermot Kenny, Antonio J. Ricco, Nigel Kent, Lourdes Basabe-Desmonts

Articles

We report the development of a microfluidic device for the rapid assay in whole blood of platelet-protein interactions indicative of the efficacy of antiplatelet drugs—e.g., aspirin and Plavix, two of the world’s most widely used drugs—in cardiovascular patients. Because platelet adhesion to surface-confined protein matrices is modulated by fluid shear rates at the blood/protein interface, and because such binding is a better indicator of platelet function than platelet self-aggregation, we designed, fabricated, and characterized the performance of a family of disposable, self-powered microfluidic chips with well-defined flow and interfacial shear rates suitable for small blood volumes (≤ 200 µL). We …

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Mapping Qtls And Association Of Differentially Expressed Gene Transcripts For Multiple Agronomic Traits Under Different Nitrogen Levels In Sorghum, Malleswari Gelli, Sharon E. Mitchell, Kan Liu, Thomas E. Clemente, Donald P. Weeks, Chi Zhang, David R. Holding, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Background: Sorghum is an important C₄ crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization.

Results: A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha⁻¹ fertilizer) and low N (0 kg.ha⁻¹ fertilizer) conditions. A linkage map spanning 1614 cM was developed …

Proteomic Profiling Of Maize Opaque Endosperm Mutants Reveals Selective Accumulation Of Lysine-Enriched Proteins, Kyla J. Morton, Shangang Jia, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Reduced prolamin (zein) accumulation and defective endoplasmic reticulum (ER) body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and Mucronate (Mc), whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. A liquid chromatography approach coupled with tandem mass spectrometry (LC-MS/MS) proteomics was used to compare non-zein proteins of nearly isogenic opaque endosperm mutants. In total, 2762 proteins were identified that were enriched for biological processes such …

Simulating Long-Term Impacts Of Cover Crops And Climate Change On Crop Production And Environmental Outcomes In The Midwestern United States, Andrea D. Basche, Sotririos V. Archontoulis, Thomas C. Kaspar, Dan B. Jaynes, Timothy B. Parkin, Fernando E. Miguez

Department of Agronomy and Horticulture: Faculty Publications

It is critical to evaluate conservation practices that protect soil and water resources from climate change in the Midwestern United States, a region that produces one-quarter of the world’s soybeans and one-third of the world’s maize. An over-winter cover crop in a maize–soybean rotation offers multiple potential benefits that can reduce the impacts of higher temperatures and more variable rainfall; some of the anticipated changes for the Midwest. In this experiment we used the Agricultural Production Systems sIMulator (APSIM) to understand how winter rye cover crops impact crop production and environmental outcomes, given future climate change. We first tested APSIM …

Decipher The Molecular Response Of Plant Single Cell Types To Environmental Stresses, Mehrnoush Nourbakhsh-Rey, Marc Libault

Department of Agronomy and Horticulture: Faculty Publications

The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress.Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, …

Organic Struggle: The Movement For Sustainable Agriculture In The United States [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Organic Struggle chronicles the challenges encountered by innovators in a growing segment of the U.S. food production and marketing system. Practiced for millennia by farmers before the introduction of chemical fertilizers and pesticides, and first developed more formally in Europe, organic farming practices began to gain prominence in the United States only in the 1950s. Far more than a system for producing food, this strategy has become a focus for those supporting healthy and pesticide-free products, for some who embrace the organic system as a food movement, and by many who disagree with the current domination of the country’s food …

Draft Genome Sequence Of Erwinia Tracheiphila, An Economically Important Bacterial Pathogen Of Cucurbits, Lori R. Shapiro, Erin D. Scully, Dana Roberts, Timothy J. Straub, Scott M. Geib, Jihye Park, Andrew G. Stephenson, Erika Salaau Rojas, Quin Liu, Gwyn Beattie, Mark Gleason, Consuelo M. De Moraes, Mark C. Mescher, Shelby G. Fleischer, Roberto Kolter, Naomi Pierce, Olga Zhaxybayeva

Department of Agronomy and Horticulture: Faculty Publications

Erwinia tracheiphila is one of the most economically important pathogens of cucumbers, melons, squashes, pumpkins, and gourds in the northeastern and midwestern United States, yet its molecular pathology remains uninvestigated. Here, we report the first draft genome sequence of an E. tracheiphila strain isolated from an infected wild gourd (Cucurbita pepo subsp. texana) plant. The genome assembly consists of 7 contigs and includes a putative plasmid and at least 20 phage and prophage elements.