Digital Commons Network^™

Amplification Of Emerging Viruses In A Bat Colony, Jan Felix Drexler, Victor Max Corman, Tom Wegner

KIP Articles

Bats host noteworthy viral pathogens, including coronaviruses, astroviruses, and adenoviruses. Knowledge on the ecology of reservoir-borne viruses is critical for preventive approaches against zoonotic epidemics. We studied a maternity colony of Myotis myotis bats in the attic of a private house in a suburban neighborhood in Rhineland-Palatinate, Germany, during 2008, 2009, and 2010. One coronavirus, 6 astroviruses, and 1 novel adenovirus were identified and monitored quantitatively. Strong and specific amplification of RNA viruses, but not of DNA viruses, occurred during colony formation and after parturition. The breeding success of the colony was significantly better in 2010 than in 2008, in …

Impact Of Prolonged Isolation On Adolescents With Drug-Susceptible Tuberculosis In Lima, Peru: A Qualitative Study, Victoria Elena Rapoport, Elmer Altamirano, Liz Senador, Milagros Wong, Catherine B. Beckhorn, Julia Coit, Stephanie D. Roche, Leonid Lecca, Jerome T. Galea, Silvia S. Chiang

Social Work Faculty Publications

Objectives Patients with tuberculosis (TB) generally are instructed to isolate at the beginning of treatment in order to prevent disease transmission. The duration of isolation varies and may be prolonged (ie, lasting 1 month or more). Few studies have examined the impact of isolation during TB treatment on adolescents, who may be more vulnerable to its negative effects.

Methods This study took place from 2018 through 2019 in Lima, Peru, where the Ministry of Health mandates the exclusion of patients with TB from educational institutions for at least 2 months. Using semi-structured guides, we conducted individual in-depth interviews with adolescents …

Land Reversion And Zoonotic Spillover Risk, John E. Vinson, Nicole L. Gottdenker, Luis Fernando Chaves, Rajreni B. Kaul, Andrew M. Kramer, John M. Drake, Richard J. Hall

Integrative Biology Faculty and Staff Publications

Deforestation alters wildlife communities and modifies human–wildlife interactions, often increasing zoonotic spillover potential. When deforested land reverts to forest, species composition differences between primary and regenerating (secondary) forest could alter spillover risk trajectory. We develop a mathematical model of land-use change, where habitats differ in their relative spillover risk, to understand how land reversion influences spillover risk. We apply this framework to scenarios where spillover risk is higher in deforested land than mature forest, reflecting higher relative abundance of highly competent species and/or increased human–wildlife encounters, and where regenerating forest has either very low or high spillover risk. We find …

Limosilactobacillus Fermentum Strain 3872: Antibacterial And Immunoregulatory Properties And Synergy With Prebiotics Against Socially Significant Antibiotic-Resistant Infections Of Animals And Humans, Vyacheslav M. Abramov, Igor V. Kosarev, Andrey V. Machulin, Tatiana V. Priputnevich, Irina O. Chikileva, Eugenia I. Deryusheva, Tatiana N. Abashina, Almira D. Donetskova, Alexander N. Panin, Vyacheslav G. Melnikov, Natalia E. Suzina, Ilya N. Nikonov, Marina V. Selina, Valentin S. Khlebnikov, Vadim K. Sakulin, Raisa N. Vasilenko, Vladimir A. Samoilenko, Vladimir N. Uversky, Andrey V. Karlyshev

Molecular Medicine Faculty Publications

Limosilactobacillus fermentum strain 3872 (LF3872) was originally isolated from the breast milk of a healthy woman during lactation and the breastfeeding of a child. The high-quality genome sequencing of LF3872 was performed, and a gene encoding a unique bacteriocin was discovered. It was established that the bacteriocin produced by LF3872 (BLF3872) belongs to the family of cell-wall-degrading proteins that cause cell lysis. The antibacterial properties of LF3872 were studied using test cultures of antibiotic-resistant Gram-positive and Gram-negative pathogens. Gram-positive pathogens (Staphylococcus aureus strain 8325-4 and S. aureus strain IIE CI-SA 1246) were highly sensitive to the bacteriolytic action of LF3872. …

Fight Fire With Fire: The Need For A Vaccine Based On Intrinsic Disorder And Structural Flexibility, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The absence of advancement in finding efficient vaccines for several human viruses, such as hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and herpes simplex viruses (HSVs) despite 30, 40, and even 60 years of research, respectively, is unnerving. Among objective reasons for such failure are the highly glycosylated nature of proteins used as primary vaccine targets against these viruses and the presence of neotopes and cryptotopes, as well as high mutation rates of the RNA viruses HCV and HIV-1 and the capability to establish latency by HSVs. However, the lack of success in utilization of the structure-based …

What Is The Recorded Economic Cost Of Alien Invasive Fishes Worldwide?, Phillip J. Haubrock, Camille Bernery, Ross N. Cuthbert, Chunlong Liu, Melina Kourantidou, Boris Leroy, Anna J. Turbelin, Andrew M. Kramer, Laura Verbrugge, Christophe Diagne, Franck Courchamp, Rodolphe E. Gozlan

Integrative Biology Faculty and Staff Publications

Invasive alien fishes have caused pernicious ecological impacts on aquatic ecosystems. However, there has not been a global appraisal of associated economic impacts. Here, we compiled reported economic impacts of invasive alien fishes using the most comprehensive global database of invasion costs (InvaCost). We analyze how fish invasion costs are distributed geographically and temporally, as well as which socioeconomic sectors are most impacted. Fish invasions have caused the economic loss of at least US$32.8 billion globally (2017 value), from only 26 reported species (of 128 known invasive alien fish species). North America had the highest costs (> 99%), followed by …

Ticks And Novel Chigger Mite Species On Passerine Birds In Southeastern Arizona, Kathleen Groschupf, James W. Mertins

Arizona Birds

We document the combined occurrences of one immature tick species (Amblyomma cf. triste), 2 known chigger mite species, Euschoengastia numerosa and Neoschoengastia americana, and 4 undescribed species of Neoschoengastia chiggers attached to individuals of 11 bird species in southeastern Arizona. Groschupf incidentally discovered clusters of the orangecolored chiggers while examining migrant and local birds for Amblyomma cf. triste, a hard tick documented as uncommon and discontinuously widespread in southeastern Arizona, southern New Mexico, West Texas, and northwestern Mexico. All of these ectoparasite collection records are new for these particular bird host species in Arizona, and Savannah Sparrow (Passerculus sandwichensis) is …

Metajournalistic Discourse As A Stabilizer Within The Journalistic Field: Journalistic Practice In The Covid-19 Pandemic, Gregory P. Perreault, Mildred F. Perreault, Phoebe Maares

School of Advertising & Mass Communications Faculty Publications

The COVID-19 Pandemic created a two-fold challenge for journalists: first, the task of gathering and distributing information vital to the responses of the public, and second, the challenge of mitigating the complexities of the journalism field. The purpose of this study is to connect the theoretical frameworks of metajournalistic discourse and field theory, using the touch point of journalistic practice. Prior research has postulated that metajournalistic discourse operates as a stabilizing force in the journalistic field. Using the timely test of the COVID-19 pandemic, this study seeks to explore the discursive construction of journalistic practice during a pandemic through the …

Bioactive Peptides: Synthesis, Sources, Applications, And Proposed Mechanisms Of Action, Mohsen Akbarian, Ali Khani, Sara Eghbalpour, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Bioactive peptides are a group of biological molecules that are normally buried in the structure of parent proteins and become active after the cleavage of the proteins. Another group of peptides is actively produced and found in many microorganisms and the body of organisms. Today, many groups of bioactive peptides have been marketed chemically or recombinantly. This article reviews the various production methods and sources of these important/ubiquitous and useful biomolecules. Their applications, such as antimicrobial, antihypertensive, antioxidant activities, blood-lipid-lowering effect, opioid role, antiobesity, ability to bind minerals, antidiabetic, and antiaging effects, will be explored. The types of pathways proposed …

Sars-Cov-2 Intermittent Virulence As A Result Of Natural Selection, Alberto Rubio-Casillas, Elrashdy M. Redwan, Vladimir N. Uversky

Molecular Medicine Faculty Publications

For the first time in history, we have witnessed the origin and development of a pandemic. To handle the accelerated accumulation of viral mutations and to comprehend the virus’ evolutionary adaptation in humans, an unparalleled program of genetic sequencing and monitoring of SARS-CoV-2 variants has been undertaken. Several scientists have theorized that, with the Omicron surge producing a more contagious but less severe disease, the end of COVID-19 is near. However, by analyzing the behavior shown by this virus for 2 years, we have noted that pandemic viruses do not always show decreased virulence. Instead, it appears there is an …

Interferon-Β Activity Is Affected By S100b Protein, Alexey S. Kazakov, Alexander D. Sofin, Nadezhda V. Avkhacheva, Eugenia I. Deryusheva, Victoria A. Rastrygina, Maria E. Permyakova, Vladimir N. Uversky, Eugene A. Permyakov, Sergei E. Permyakov

Molecular Medicine Faculty Publications

Interferon-β (IFN-β) is a pleiotropic cytokine secreted in response to various pathological conditions and is clinically used for therapy of multiple sclerosis. Its application for treatment of cancer, infections and pulmonary diseases is limited by incomplete understanding of regulatory mechanisms of its functioning. Recently, we reported that IFN-β activity is affected by interactions with S100A1, S100A4, S100A6, and S100P proteins, which are members of the S100 protein family of multifunctional Ca2+-binding proteins possessing cytokine-like activities (Int J Mol Sci. 2020;21(24):9473). Here we show that IFN-β interacts with one more representative of the S100 protein family, the S100B protein, involved in …

Early Taurine Administration As A Means For Halting The Cytokine Storm Progression In Covid-19 Patients, Alberto Rubio-Casillas, Ramesh C. Gupta, Elrashdy M. Redwan, Vladimir N. Uversky, Raied A. Badierah

Molecular Medicine Faculty Publications

Around the world, more than 6.2 million individuals have died as a result of coronavirus disease 2019 (COVID-19). According to a recent survey conducted among immunologists, epidemiologists, and virologists, this disease is expected to become endemic. This implies that the disease could have a continuous presence and/or normal frequency in the population. Pharmacological interventions to prevent infection, as well as to treat the patients at an early phase of illness to avoid hospitalization are essential additions to the vaccines. Taurine is known to inhibit the generation of all inflammatory mediators linked to the cytokine storm. It can also protect against …

Nanoparticles For Coronavirus Control, Maryam Kianpour, Mohsen Akbarian, Vladimir N. Uversky

Molecular Medicine Faculty Publications

More than 2 years have passed since the SARS-CoV-2 outbreak began, and many challenges that existed at the beginning of this pandemic have been solved. Some countries have been able to overcome this global challenge by relying on vaccines against the virus, and vaccination has begun in many countries. Many of the proposed vaccines have nanoparticles as carriers, and there are different nano-based diagnostic approaches for rapid detection of the virus. In this review article, we briefly examine the biology of SARS-CoV-2, including the structure of the virus and what makes it pathogenic, as well as describe biotechnological methods of …

Patient And Provider Perceptions Of A Community-Based Accompaniment Intervention For Adolescents Transitioning To Adult Hiv Care In Urban Peru: A Qualitative Analysis, Jerome T. Galea, Milagros Wong, Brennan Ninesling, Alicia Ramos, Liz Senador, Hugo Sanchez, Lenka Kolevic, Eduardo Matos, Eduardo Sanchez, Renato A. Errea, Andrew Lindeborg, Carlos Benites, Leonid Lecca, Sonya Shin, Molly F. Franke

Social Work Faculty Publications

Introduction: Adolescents living with HIV (ALWH) experience higher mortality rates compared to other age groups, exacerbated by the suboptimal transition from paediatric to adult HIV care, during which decreased adherence to antiretroviral therapy (ART) and unsuppressed viremia are frequent. Care transition—a process lasting months or years—ideally prepares ALWH for adult care and can be improved by interventions that are youth-friendly and address psychosocial issues affecting ART adherence; however, such interventions are infrequently operationalized. Community-based accompaniment (CBA), in which laypeople provide individualized support and health system navigation, can improve health outcomes among adults with HIV. Here, we describe patient and provider …

Geographic Accessibility To Health Facilities Predicts Uptake Of Community-Based Tuberculosis Screening In An Urban Setting, Helen E. Jenkins, Sally Ayuk, Daniela Puma, Meredith B. Brooks, Ana Karina Millones, Judith Jimenez, Leonid Lecca, Jerome T. Galea, Mercedes Becerra, Salmaan Keshavjee, Courtney M. Yuen

Social Work Faculty Publications

Objectives: Annually, more than 30% of individuals with tuberculosis (TB) remain undiagnosed. We aimed to assess whether geographic accessibility measures can identify neighborhoods that would benefit from TB screening services targeted toward closing the diagnosis gap.

Methods: We used data from a community-based mobile TB screening program in Carabayllo district, Lima, Peru. We constructed four accessibility measures from the geographic center of neighborhoods to health facilities. We used logistic regression to assess the association between these measures and screening uptake in one's residential neighborhood versus elsewhere, with quasi-information criterion values to assess the association.

Results: We analyzed the screening locations …

Higher Native Peruvian Genetic Ancestry Proportion Is Associated With Tuberculosis Progression Risk, Samira Asgari, Yang Luo, Chuan-Chin Huang, Zibiao Zhang, Roger Calderon, Carmen Contreras, Jerome T. Galea, Leonid Lecca, David Jones, D. Branch Moody, Megan B. Murray, Soumya Raychaudhuri

Social Work Faculty Publications

No abstract provided.

The Role Of Influential Actors In Fostering The Polarized Covid-19 Vaccine Discourse On Twitter: Mixed Methods Of Machine Learning And Inductive Coding, Loni Hagen, Ashley Fox, Heather O'Leary, Deandre Dyson, Kimberly Walker, Cecile A. Lengacher, Raquel Hernandez

School of Information Faculty Publications

Background: Since COVID-19 vaccines became broadly available to the adult population, sharp divergences in uptake have emerged along partisan lines. Researchers have indicated a polarized social media presence contributing to the spread of mis- or disinformation as being responsible for these growing partisan gaps in uptake.

Objective: The major aim of this study was to investigate the role of influential actors in the context of the community structures and discourse related to COVID-19 vaccine conversations on Twitter that emerged prior to the vaccine rollout to the general population and discuss implications for vaccine promotion and policy.

Methods: We collected tweets …

Integrating Multiple Survey Techniques To Document A Shifting Bat Community In The Wake Of White-Nose Syndrome, D. Scott Reynolds, Kevin Shoemaker, Susi Von Oettingen, Stephen Najjar, Jacques P. Veilleux, Paul R. Moosman Jr

KIP Articles

The long-term study of bat communities often depends on a diverse set of sampling methodologies that are chosen based on the species or habitat management priorities of the research project. Integrating the data from a diverse set of methodologies (such as acoustic monitoring and mist net sampling) would improve our ability to characterize changes in community structure or composition over time, such as one would expect following an emergent infectious disease such as white-nose syndrome. We developed a Bayesian state-space model to integrate these disparate data into a common currency (relative abundance). We collected both acoustic monitoring and mist net …

Using Artificial Intelligence To Decipher Epigenetic Code Of Drug Resistance In The Deadliest Human Malaria Parasite, Samira Jahangiri

USF Tampa Graduate Theses and Dissertations

Malaria remains one of the immense global public health challenges, with an estimated ~200 million cases worldwide in 2019 despite the remarkable gains in reducing this deadly disease over the past decade. The recent emergence and spread of artemisinin resistance (ART-R) in Plasmodium falciparum will increasingly impede global efforts to control and eliminate malaria. Previous studies have observed broad transcriptional changes and identified several noncoding genetic variants strongly associated with ART-R. The broad transcriptional variations suggest that the malaria parasite uses sophisticated epigenetic regulation to survive under drug pressure. Therefore, evaluating the regulatory effects of noncoding-variants in malaria parasites is …

Mobile Colorimetric Assay Device, Anna Pyayt, Arsenii Zhdanov, Jordan Keefe, Luis Franco-Waite

USF Patents

A mobile phone-based system for ELISA (MELISA). The MELISA system can perform all steps of ELISA procedure and output hormone concentration values. The system includes a heater that keeps the temperature required for sample incubation, illumination system for sample image capturing, and a digital camera system. All components are enclosed in a dark box to create optimal light conditions for image capturing. After sample images are captured, they are digitally processed, and hormone concentration values are reported based on colorimetric data from the samples. The system can be used to complete all steps of the assay, including incubation and reading. …

A Biocultural Analysis Of The Impacts Of Interactions Between West Africans And Europeans During The Trans-Atlantic Trade At Elmina, Ghana, Heidi Ellen Miller

USF Tampa Graduate Theses and Dissertations

This project utilizes a biocultural approach to assess the demographics and health of the West African population from Elmina, Ghana. Elmina, selected by the Portuguese in 1482 as the site of the first European trade fort in sub-Saharan Africa, grew from a small coastal fishing village to a large settlement over the course of more than 400 years of trade and cultural entanglement. Taken over by the Dutch and then ceded to the British, the people of Elmina navigated significant cultural changes, changes and experiences that can be detected in their skeletal remains. Bioarchaeological research concerned with the effects of …

Infectious Disease Modeling And Intervention Planning, Shalome Hanisha Anand Tatapudi

USF Tampa Graduate Theses and Dissertations

Disease outbreaks caused by existing and emerging pathogens pose a serious threat to local and global communities in the form of epidemics and pandemics, respectively. The 2009 H1N1 pandemic and the 2019 COVID-19 pandemic are exemplars of how underprepared both the developed and developing nations are at mitigating pandemics.

Mathematical modeling and simulation of disease outbreaks has served as a powerful tool to understand disease transmission dynamics. They also aid in developing effective intervention strategies. However, existing models are usually particularized to a region, or a specific disease pathogen and interventions used in these models may not translate well to …

Learning Connections Inventory© Validation Using A Physician Assistant Training Program, Roberta Worsham

USF Tampa Graduate Theses and Dissertations

The purpose of this study was to validate the Learning Connections Inventory for use with the military Physician Assistant students at the Interservice Physician Assistant Program at Fort Sam Houston, TX. The 61 participants in this study completed both a demographic survey and the Learning Connections Inventory (LCI©). The results of the demographic questionnaire depicted the characteristics of the participants and the LCI© described the learning patterns of each participant.

Research Questions one, confirmation of the current LCI© model, and two, the instructor assessment and the current model agreement, were answered using confirmatory factor analysis (CFA) and construct validity. The …

Experimental Challenge Of A North American Bat Species, Big Brown Bat (Eptesicus Fuscus), With Sars-Cov-2, Jeffrey S. Hall, Susan Knowles, Sean W. Nashold, Hon S. Ip, Ariel E. Leon, Tonie Rocke, Saskia Keller, Mariano Carossino, Udeni Balasuriya, Erik Hofmeister

KIP Articles

No abstract provided.

Microbial Dark Matter: Culturing The Uncultured In Search Of Novel Chemotaxonomy, Sarah J. Kennedy

USF Tampa Graduate Theses and Dissertations

Although <1% of environmental isolates can be cultured, insights into the culturable fraction refine future techniques to unlock the cryptic biodiversity. This cryptic biodiversity is omnipresent within culture-independent surveys of environmental bacterial populations. Subsequently, these elusive organisms are termed “microbial dark matter” due to the intrigue surrounding their potential taxonomic and biosynthetic impacts. To this end of investigating bacterial-specific dark matter, we employed high-throughput culturing techniques to examine Gulf of Mexico sediments and sponges for chemotaxonomically important bacteria. Through stepwise implementation of permissive and selective recovery techniques, we succeeded in recovering over 150 unique bacterial isolates. We observed several isolates that pose as chemotaxonomically interesting, including several strains that belong to critical bioremediation taxa. In addition to these biotechnological-amenable isolates, we have also succeeded in culturing taxa historically attributed with antibacterial discoveries. One such isolate was a previously sponge-associated organism belonging to the rarely cultured Verrucosispora genus. Through extensive comparative genomics, we identified it as a novel species and subsequently named it Verrucosispora sioxanthis sp. nov. with the published genome serving as a resource for continued microbial dark matter investigations. Following continued passaging of the organism, we observed improved growth, biomass, and liquid growth dispersal within each increasingly sub-passaged generation of the isolate. As such, the laboratory attenuation, or domestication, of the organism warranted in-depth whole genomic analyses to generate insight into the increased laboratory sustainability. Through phenotypically-guided bioinformatics, we determined that the domestication was mediated through genome-wide selective pseudo- or non-pseudogenization of genes. As the previously sponge-associated organism evolved with the selection pressures of the static laboratory, we demonstrate that isolate effectively underwent genomic atrophy to resolve into a largely stable, sustainable laboratory-domesticated strain. Collectively, our chemotaxonomic discovery pipeline expands on the culturable bacterial biodiversity and ultimately provides a previously uncultured model organism for initial forays into resolving the microbial dark matter knowledge gap.

Investigation Of An Alternative Protocol For The Production Of Sars-Cov-2 Antigenic Proteins, Nichole Ninaltowski

USF Tampa Graduate Theses and Dissertations

With the COVID-19 pandemic showing no signs of slowing down, large-scale antigenic protein production is still needed for surveillance using serologic assays. From screening to vaccines to biotherapeutics, being able to produce the proteins for these assays is essential; however, the current gold standard method for producing SARS-CoV-2 spike proteins is prohibitively expensive for most research groups.

Alternative methods of transfecting mammalian cells to produce recombinant proteins that are relatively inexpensive have been used for years. Unlike the expensive, commercially available lipid-based methods, other established methods such as polyethyleneimine (PEI), are considerably easier, and cheaper to meet the needs of …

Seasonality In Competence To Transmit West Nile Virus For A Widespread Reservoir, Kyle L. Koller

USF Tampa Graduate Theses and Dissertations

All organisms face a central conflict; a limited supply of resources must beoptimally allocated to competing biological functions. Utilizing robust immune defenses can be energetically costly;, thus, immune function is often diminished when other processes, such as reproduction, molt, or migration demand energy. As wild animals residing in temporally dynamic environments face seasonal patterns in resource availability, infectious disease risk, and environmental suitability, many species have evolved endogenous biological rhythms so that the performance of reproduction, molt, or migration and the associated trade-off with immune function be completed when doing so best promotes fitness. In turn, this demand to optimize …

Synthesis Of A Multimodal Ecological Model For Scalable, High-Resolution Arboviral Risk Prediction In Florida, Sean P. Beeman

USF Tampa Graduate Theses and Dissertations

West Nile virus (WNV) and Eastern Equine Encephalitis virus (EEEV) represent the two greatest endemic arboviral risks to the state of Florida. Currently, no approved human vaccine exists for the prevention of either virus. In the absence of a vaccine, effective disease surveillance is paramount for public health. In Florida, WNV and EEEV sentinel chicken surveillance is conducted by mosquito control programs operated at the county, municipality, or special taxing district level. This program was implemented in 1978 following human outbreaks of St. Louis Encephalitis virus (SLEV) that occurred between 1959 and 1977, with initial sentinel coops placed in proximity …

Systems And Methods For Detecting Alcohol, Acetone, And Carbon Monoxide In Breath, Tiffany Crystal Miller, Salvatore Domenic Morgera, Stephen Edward Saddow, Arash Takshi

USF Patents

A breath collection device can detect changes associated with pathogenesis of a disease, such as COVID-19, including biomarkers of immune response for respiratory symptoms, central nervous system injury, and/or peripheral nervous system injury in user breath and/or odor. The breath collection device can detect concentrations of alcohol, acetone, and carbon monoxide in user breath samples. A breath sample can be received in an internal bladder of the device for sensor analysis. Concentrations of alcohol, acetone, and carbon monoxide can be determined by calibrated calculation. A detection method for alcohol, acetone, and carbon monoxide can provide a non-invasive, rapid, and selective …

Futurizing Gastronomic Experiences In Natural Environments, Francesc Fusté-Forné

Journal of Sustainability and Resilience

The current pandemic accentuated the need for a more responsible tourism system, where local food production and consumption become a cornerstone of sustainable tourism futures. Experiences embedded in natural environments are neither new nor recent, but the pandemic urged tourism stakeholders to look at nature again as a source of inspiration for tourism regeneration. The research analyses the configuration of gastronomic experiences in protected areas through the philosophy of a gourmet restaurant located in a volcanic setting in Catalonia, north-eastern Spain.