Digital Commons Network^™

Novel Circular Single-Stranded Dna Viruses Identified In Marine Invertebrates Reveal High Sequence Diversity And Consistent Predicted Intrinsic Disorder Patterns Within Putative Structural Proteins, Karyna Rosario, Ryan Schenck, Rachel Harbeitner, Stephanie Lawler, Mya Breitbart

Marine Science Faculty Publications

Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. …

Reduction Of Nutrients, Microbes, And Personal Care Products In Domestic Wastewater By A Benchtop Electrocoagulation Unit, E. Symonds, M. Cook, S. Mcquaig, R. Ulrich, R. Schenck, J. Lukasik, E. Van Vleet, Mya Breitbart

Marine Science Faculty Publications

To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic …

Potential Habitat Of Acropora Spp. On Reefs Of Florida, Puerto Rico, And The Us Virgin Islands, Katherine Wirt

Marine Science Faculty Publications

Elkhorn and staghorn corals (Acropora palmata, Acropora cervicornis) were listed in 2006 as threatened under the Endangered Species Act. The goal of this study was to create model potential-habitat maps for A. palmata and A. cervicornis, while identifying areas for possible re-establishment. These maps were created using a database of reported field observations in combination with existing benthic habitat maps. The mapped coral reef and hardbottom classifications throughout Florida, Puerto Rico, and the US Virgin Island reef tracts were used to generate potential-habitat polygons using buffers that incorporated 95% and 99% of reported observations of Acropora spp. …

Structure And Stability Of Recombinant Bovine Odorant-Binding Protein: I. Design And Analysis Of Monomeric Mutants, Olga V. Stepanenko, Denis O. Roginskii, Olesya V. Stepanenko, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov

Molecular Medicine Faculty Publications

Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and to understand the role of the domain swapping on maintaining the native structure of the protein, structural properties of the recombinant wild type bOBP and its mutant that cannot dimerize via the domain swapping were analyzed. We also looked at the effect of the disulfide bond by designing a monomeric bOBPs with restored disulfide bond which is conserved in other lipocalins. Finally, to …

Does Intrinsically Disordered Caldesmon Bind Calmodulin Via The “Buttons On A String” Mechanism?, Sergei E. Permyakov, Eugene A. Permyakov, Vladimir N. Uversky

Molecular Medicine Faculty Publications

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636-771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A, W707A, and W737A) and a double tryptophan mutant (W674A/W707A) suggested that although the interaction of CaD136 with calmodulin (CaM) can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136 tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be …

Does Intrinsically Disordered Caldesmon Bind Calmodulin Via The “Buttons On A String” Mechanism?, Sergei E. Permyakov, Eugene A. Permyakov, Vladimir N. Uversky

Molecular Medicine Faculty Publications

We show here that chicken gizzard caldesmon (CaD) and its C-terminal domain (residues 636-771, CaD136) are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A, W707A, and W737A) and a double tryptophan mutant (W674A/W707A) suggested that although the interaction of CaD136 with calmodulin (CaM) can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136 tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be …

Identification Of Proteins Associated With Amyloidosis By Polarity Index Method., Carlos Polanco, José Lino Samaniego, Vladimir N N. Uversky, Jorge Alberto Castañón-González, Thomas Buhse, Marili Leopold-Sordo, Alejandro Madero-Arteaga, Alicia Morales-Reyes, Lourdes Tavera-Sierra, Jesus A. González-Bernal, Miguel Arias-Estrada

Molecular Medicine Faculty Publications

There is a natural protein form, insoluble and resistant to proteolysis, adopted by many proteins independently of their amino acid sequences via specific misfolding-aggregation process. This dynamic process occurs in parallel with or as an alternative to physiologic folding, generating toxic protein aggregates that are deposited and accumulated in various organs and tissues. These proteinaceous deposits typically represent bundles of β-sheet-enriched fibrillar species known as the amyloid fibrils that are responsible for serious pathological conditions, including but not limited to neurodegenerative diseases, grouped under the term amyloidoses. The proteins that might adopt this fibrillar conformation are some globular proteins and …

Intrinsically Disordered Proteins In The Nucleus Of Human Cells, Telma Frege, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the …

Solvent Properties Of Water In Aqueous Solutions Of Elastin-Like Polypeptide, Luisa A. Ferreira, James T. Cole, Christian Reichardt, Nolan B. Holland, Vladimir N. Uversky, Boris Y. Zaslavsky

Molecular Medicine Faculty Publications

The phase-transition temperatures of an elastin-like polypeptide (ELP) with the (GVGVP)₄₀ sequence and solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity in its aqueous solutions were quantified in the absence and presence of different salts (Na₂SO₄, NaCl, NaClO₄, and NaSCN) and various osmolytes (sucrose, sorbitol, trehalose, and trimethylamine N-oxide (TMAO)). All osmolytes decreased the ELP phase-transition temperature, whereas NaCl and Na₂SO₄ decreased, and NaSCN and NaClO₄ increased it. The determined phase-transition temperatures may be described as a linear combination of the solvent’s dipolarity/polarizability and hydrogen-bond donor acidity. The …

Identifying Similar Patterns Of Structural Flexibility In Proteins By Disorder Prediction And Dynamic Programming, Aidan Petrovich, Adam Borne, Vladimir N. Uversky, Bin Xue

Molecular Medicine Faculty Publications

Computational methods are prevailing in identifying protein intrinsic disorder. The results from predictors are often given as per-residue disorder scores. The scores describe the disorder propensity of amino acids of a protein and can be further represented as a disorder curve. Many proteins share similar patterns in their disorder curves. The similar patterns are often associated with similar functions and evolutionary origins. Therefore, finding and characterizing specific patterns of disorder curves provides a unique and attractive perspective of studying the function of intrinsically disordered proteins. In this study, we developed a new computational tool named IDalign using dynamic programming. This …

Coral–Algal Phase Shifts Alter Fish Communities And Reduce Fisheries Production, Cameron H. Ainsworth, Peter J. Mumby

Marine Science Faculty Publications

Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One …

Colored Dissolved Organic Matter In The Coastal Ocean: An Optical Tool For Coastal Zone Environmental Assessment And Management, Paula Coble, Chuanmin Hu, Richard W. Gould Jr., Grace Chang, A. Michelle Wood

Marine Science Faculty Publications

The phrase “deep blue sea” is so common in English usage that all three words are individually synonymous for “ocean.” Poems, song titles, and movies, have used these words to conjure up images that few people have observed firsthand. The real “deep blue sea” can typically be seen only hundreds of miles offshore. The areas of the ocean that most people are able to observe are coastal waters, which are rarely “deep,” and only in the cleanest, clearest regions of the world, such as along the coast of Australia, do these waters appear blue. Soil runoff from rivers, algal blooms, …

A Harmful Algal Bloom Of Karenia Brevis In The Northeastern Gulf Of Mexico As Revealed By Modis And Viirs: A Comparison, Chuanmin Hu, Brian B. Barnes, Lin Qi, Alina A. Corcoran

Marine Science Faculty Publications

The most recent Visible Infrared Imager Radiometer Suite (VIIRS) is not equipped with a spectral band to detect solar-stimulated phytoplankton fluorescence. The lack of such a band may affect the ability of VIIRS to detect and quantify harmful algal blooms (HABs) in coastal waters rich in colored dissolved organic matter (CDOM) because of the overlap of CDOM and chlorophyll absorption within the blue-green spectrum. A recent HAB dominated by the toxin-producing dinoflagellate Karenia brevis in the northeastern Gulf of Mexico, offshore of Florida’s Big Bend region, allowed for comparison of the capacities of VIIRS and Moderate Resolution Imaging Spectroradiometer (MODIS) …

Teaching High School Biology Students To Coordinate Text And Diagrams: Relations With Transfer, Effort, And Spatial Skill, Bradley W. Bergey, Jennifer G. Cromley, Nora S. Newcombe

Publications and Research

There is growing evidence that targeted instruction can improve diagram comprehension, yet one of the skills identified in the diagram comprehension literature—coordinating multiple representations —has rarely been directly taught to students and tested as a classroom intervention. We created a Coordinating Multiple Representation (CMR) intervention that was an addition to an intervention focused on Conventions of Diagrams (COD) and tested their joint effects on diagram comprehension for near transfer (uninstructed biology diagrams), far transfer (uninstructed geology diagrams), and content learning (biology knowledge). The comparison group received instruction using a previously validated intervention that focused exclusively on COD. Participants were 9th–10th …

2015 Accountability Report Usf Sarasota-Manatee, Usf

USF Accountability Reports

No abstract provided.

2015 Work Plan Usf Sarasota-Manatee, Usf

USF Accountability Reports

No abstract provided.

2015 Work Plan Usf System, Usf

USF Accountability Reports

No abstract provided.

Uis Bulletin, Volume 57, January 2015, Efraín Mercado

UIS Bulletin

Contents: Editorial: 50 Years of UIS - A Time to Celebrate -- Report of Commission on Arts and Letters -- Report of Commission on Cave Diving -- XVth International Symposium of Speleotherapy -- Report of Commission on Cave Rescue -- Informatics Commission: Help for building new cave/karst database -- Cave record project in Portugal -- Report of Commission on History of Speleology -- In memoriam: Yaroslav Chonka -- In memoriam: Brother Nicholas Sullivan -- International Workshop on Ice Caves VI (USA) -- First Congress on Roman Mining (Portugal) -- Turismo Inclusivo (Inclusive Tourism) -- Minutes of the UIS Bureau meeting …

Live, Work, Play: Fy 2015 Annual Report, Tennessee. Department Of Environment And Conservation

TDEC Annual Reports

This annual report highlights the accomplishments of the Tennessee Department of Environment and Conservation over the fiscal year.

Environmental Monitoring Report 2015, Tennessee. Department Of Environment And Conservation

Environmental Monitoring Reports

The Tennessee Department of Environment and Conservation (TDEC), Division of Remediation, Oak Ridge Office (TDEC), is providing an annual environmental monitoring report for the calendar year 2015 under terms of the Tennessee Oversight Agreement (TOA) between the state of Tennessee and the United States Department of Energy (DOE), Section A.7.2.1. This monitoring report will focus on radiological emissions and releases, mercury monitoring and releases, monitoring of decommissioning and demolishing (D&D) remedial activities, Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) landfills, oversight of impacts to regional

Numeracy Infusion Course For Higher Education (Niche), 1: Teaching Faculty How To Improve Students' Quantitative Reasoning Skills Through Cognitive Illusions, Frank Wang, Esther I. Wilder

Publications and Research

We describe one of the eight units of a professional development program, the Numeracy Infusion Course for Higher Education (NICHE), which introduces research on cognition, including dual-processing theories, to university faculty. Under the dual-processing framework, System 1 (intuition) quickly proposes intuitive answers to judgment problems as they arise, while System 2 (deliberation) monitors the quality of these proposals, which it may endorse, correct, or override. We present several classic questions that demonstrate the pitfalls of overreliance on intuition without analytical thinking, then describe faculty participants’ responses to these questions and their ideas on how to apply cognitive illusion research to …

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

Caring Minds

No abstract provided.

From Research Into Policy And Practice: Annual Report 2014, Population Council

Annual Reports

No abstract provided.

Characterization Of Novel Sorghum Brown Midrib Mutants From An Ems-Mutagenized Population, Scott E. Sattler, Ana Saballos, Zhanguo Xin, Deanna L. Funnell-Harris, Wilfred Vermerris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Reducing lignin concentration in lignocellulosic biomass can increase forage digestibility for

ruminant livestock and saccharification yields of biomass for bioenergy. In sorghum (Sorghum bicolor (L.) Moench) and several other C4 grasses, brown midrib (bmr) mutants have been shown to reduce lignin concentration. Putative bmr mutants isolated from an EMS-mutagenized population were characterized and classified based on their leaf midrib phenotype and allelism tests with the previously described sorghum bmr mutants bmr2, bmr6, and bmr12. These tests resulted in the identification of additional alleles of bmr2, bmr6, and bmr12, and, in addition, six bmr …

Assessment Of Rice Self-Sufficiency In 2025 In Eight African Countries, P. A.J. Van Oort, K. Saito, E. Amovin-Assagba, Lenny G.J. Van Bussel, Justin Van Wart, Hugo De Groot, Martin K. Van Ittersum, Kenneth Cassman, M. C.S. Wopereis

Department of Agronomy and Horticulture: Faculty Publications

Most African countries are far from self-sufficient in meeting their rice consumption; in eight countries the production: consumption ratio, ranged from 0.16 to 1.18 in 2012. We show that for the year 2025, with population growth, diet change and yield increase on existing land (intensification), countries cannot become fully self-sufficient in rice. This implies that for the future, a mixture of area expansion and imports will be needed on top of yield gap closure. Further research is needed for identification of most suitable new land for rice area expansion and areas that should be protected.

Patch Burning: Implications On Water Erosion And Soil Properties, Altingul Ozaslan Parlak, Mehmet Parlak, Humberto Blanco-Canqui, Walter H. Schacht, John A. Guretzky, Martha Mamo

Department of Agronomy and Horticulture: Faculty Publications

Patch burning can be a potential management tool to create grassland heterogeneity and enhance forage productivity and plant biodiversity, but its impacts on soil and environment have not been widely documented. In summer 2013, we studied the effect of time after patch burning (4 mo after burning [recently burned patches], 16 mo after burning [older burned patches], and unburned patches [control]) on vegetative cover, water erosion, and soil properties on a patch-burn experiment established in 2011 on a Yutan silty clay loam near Mead, NE. The recently burned patches had 29 ± 8.0% (mean ± SD) more bare ground, 21 …

Encouraging Latino Students Through Relational Teaching: A Case Study In Lawrence, Massachusetts, Ohilda Difo

MA IDS Thesis Projects

Within the next 10 years, the majority-minority ratio in the United States will shift, and people of color will outnumber white Americans. In 2014, for the first time in history, a majority of students in K-12 were children of color. Although the student demographic of public schools has changed, the demographic of teachers and the style of teaching remain archaic and catered to white students. This qualitative study focuses on the lowest educated population in the U.S. – Latino youth. The project is a case study on a highly concentrated Latino community in the city of Lawrence, Massachusetts, where 71% …

Disaster Preparedness Plan For The Study Abroad Student: How To Engage Students In Hazard Preparedness, Kimberly Ligon

MA IDS Thesis Projects

In today’s world, hazard preparedness is vital for creating disaster resilient communities across the globe. This is needed now more than ever, due to the increasing number of disasters occurring worldwide (Chafe, 2007; Nakagawa & Shaw, 2004). This culminating project researches individual and community disaster preparedness, especially preparedness in the higher education community, and specifically study abroad individuals. There is a void in the current literature on disaster preparedness for study abroad students; a community of students that is growing and could encounter more hazards than on-campus students. Through case studies of disaster resistant universities and a proposed intervention, this …

Individual Strength-Based Assessment For Adult Empowerment Ngos, Ashley T. Turner

MA IDS Thesis Projects

The purpose of this culminating comprehensive project is to advise adult empowerment focused NGOs on the importance of identifying and leveraging the strengths of the individuals they serve. Given the evidence that all individuals innately have strengths, it is important to be aware of them in order to properly engage such assets. Character strengths are studied in this paper as one of the main pillars in the field of positive psychology. This culminating comprehensive project reviews the literature on positive psychology to best understand how empowerment can be achieved. Accompanying this research is a sample resource guide that was designed …

A Nuclear Fraction Of Turnip Crinkle Virus Capsid Protein Is Important For Elicitation Of The Host Resistance Response, Sung-Hwan Kang, Feng Qu, Thomas J. Morris

Nebraska Center for Virology: Faculty Publications

The N-terminal 25 amino acids (AAs) of turnip crinkle virus (TCV) capsid protein (CP) are recognized by the resistance protein HRT to trigger a hypersensitive response (HR) and systemic resistance to TCV infection. This same region of TCV CP also contains a motif that interacts with the transcription factor TIP, as well as a nuclear localization signal (NLS). However, it is not yet known whether nuclear localization of TCV CP is needed for the induction of HRT-mediated HR and resistance. Here we present new evidence suggesting a tight correlation between nuclear inclusions formed by CP and the manifestation of HR. …