Matching Items (99)
Description
Poxviruses such as monkeypox virus (MPXV) are emerging zoonotic diseases. Compared to MPXV, Vaccinia virus (VACV) has reduced pathogenicity in humans and can be used as a partially protective vaccine against MPXV. While most orthopoxviruses have E3 protein homologues with highly similar N-termini, the MPXV homologue, F3, has a start codon mutation leading to an N-terminal truncation of 37 amino acids. The VACV protein E3 consists of a dsRNA binding domain in its C-terminus which must be intact for pathogenicity in murine models and replication in cultured cells. The N-terminus of E3 contains a Z-form nucleic acid (ZNA) binding domain and is also required for pathogenicity in murine models. Poxviruses produce RNA transcripts that extend beyond the transcribed gene which can form double-stranded RNA (dsRNA). The innate immune system easily recognizes dsRNA through proteins such as protein kinase R (PKR). After comparing a vaccinia virus with a wild-type E3 protein (VACV WT) to one with an E3 N-terminal truncation of 37 amino acids (VACV E3Δ37N), phenotypic differences appeared in several cell lines. In HeLa cells and certain murine embryonic fibroblasts (MEFs), dsRNA recognition pathways such as PKR become activated during VACV E3Δ37N infections, unlike VACV WT. However, MPXV does not activate PKR in HeLa or MEF cells. Additional investigation determined that MPXV produces less dsRNA than VACV. VACV E3Δ37N was made more similar to MPXV by selecting mutants that produce less dsRNA. By producing less dsRNA, VACV E3Δ37N no longer activated PKR in HeLa or MEF cells, thus restoring the wild-type phenotype. Furthermore, in other cell lines such as L929 (also a murine fibroblast) VACV E3Δ37N, but not VACV WT infection leads to activation of DNA-dependent activator of IFN-regulatory factors (DAI) and induction of necroptotic cell death. The same low dsRNA mutants demonstrate that DAI activation and necroptotic induction is independent of classical dsRNA. Finally, investigations of spread in an animal model and replication in cell lines where both the PKR and DAI pathways are intact determined that inhibition of both pathways is required for VACV E3Δ37N to replicate.
ContributorsCotsmire, Samantha (Author) / Jacobs, Bertram L (Thesis advisor) / Varsani, Arvind (Committee member) / Hogue, Brenda (Committee member) / Haydel, Shelley (Committee member) / Arizona State University (Publisher)
Created2021
Description
Bats are a highly diverse mammal species with a dense virome and fascinating immune system. The following project utilizes metagenomics in order to identify DNA viruses present in populations of silver-haired bats and Mexican free-tailed bats from southern Arizona. A significant number of DNA viruses and novel viruses were identified in the Cressdnaviricota phylum and Microvirdae family.
ContributorsHarding, Ciara (Author) / Varsani, Arvind (Thesis director) / Dolby, Greer (Committee member) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Watts College of Public Service & Community Solut (Contributor)
Created2022-05
Description
Wild horses have roamed the Salt River in Mesa, Arizona since the early 1800s and contribute to the great diversity of the region. Conservation of the herd has been a primary focus for many years and a current focus is population stabilization, but little is known about their virome. Circoviridae, Genomoviridae, and Smacoviridae are the three Cressdnaviricota viruses that have been identified in horses to date. Smacoviridae is classified by the rolling circle replication-associated proteins (Rep) and has a small (2.3-2.9kb), circular, single-stranded genome. The goal of this study was to identify DNA viruses within the fecal samples of the Salt River horses. Samples were collected along the lower Salt River and analyzed in the lab using a metagenomics approach. There were 422 full novel genomes of smacoviruses detected across all samples that were grouped into 144 species based on the similarity of the pairwise identity. Phylogenetic analysis shows the smacoviruses from this study fall into 3 classified genera and the rest cluster into 11 new clades. These results expand the viral diversity associated with wild horses and Smacoviridae, and further studies are needed to determine the host of these viruses.
ContributorsMcGraw, Hannah (Author) / Varsani, Arvind (Thesis director) / Murphree, Julie (Committee member) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2024-05
Description
Scorpions are predatory arachnids that are among the most ancient terrestrial invertebrates. They are typically found residing in desert and riparian environments. Viruses associated with scorpions have been explored in the past, unveiling partial RNA virus sequences and polyomaviruses, but more research in this area is necessary. Cycloviruses are non-enveloped viruses with circular single-stranded DNA genomes (~1.7 to 1.9 kb). Cycloviruses were initially identified in mammals and have now been detected in samples from a wide range of mammalian and insect species. Polyomaviruses are double-stranded DNA viruses (~4 to 7 kb). They are known for causing tumors in the host it infects, and have previously been identified in a diverse array of organisms, including scorpions. The objective for this study was to identify known and novel viruses in scorpions. Using high-throughput sequencing and traditional molecular techniques we determine the genome sequences of cycloviruses and polyomaviruses. Sixteen of the forty-three scorpion samples were positive for eight different species of cycloviruses. According to ICTV guidelines, seven of the eight species were novel cycloviruses which were found in bark scorpions, stripe-tailed scorpions, yellow ground scorpions, and giant hairy scorpions (Centruroides sculpturatus, Paravaejovis spinigerus, Paravaejovis confusus & Hadrurus arizonensis) from Maricopa, Pinal, and Pima county in Arizona, USA. Additionally, one previously known cyclovirus species was recovered in bark scorpions (Centruroides sculpturatus) in Pima county which had previously been documented in guano from a Mexican free-tailed bat in Arizona. There were ten scorpions out of forty-three for which we recovered polyomavirus scorpion samples that grouped into four different polyomavirus species. Polyomaviruses were only identified in bark scorpions (Centruroides sculpturatus) from Maricopa, Pinal, and Pima county. Of the polyomavirus genomes recovered three belong to previously identified scorpion polyomavirus 1 and five to scorpion polyomavirus 3, and two represent two new species named scorpion polyomavirus 4 and scorpion polyomavirus 5. The implications of the discovery of cycloviruses and polyomaviruses from this study contributes to our understanding of viral diversity associated with Scorpions.
ContributorsGomez, Magali (Author) / Neil, Julia (Co-author) / Varsani, Arvind (Thesis director) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Life Sciences (Contributor)
Created2024-05
Description
Scorpions are predatory arachnids that are among the most ancient terrestrial invertebrates. They are typically found residing in desert and riparian environments. Viruses associated with scorpions have been explored in the past, unveiling partial RNA virus sequences and polyomaviruses, but more research in this area is necessary. Cycloviruses are non-enveloped viruses with circular single-stranded DNA genomes (~1.7 to 1.9 kb). Cycloviruses were initially identified in mammals and have now been detected in samples from a wide range of mammalian and insect species. Polyomaviruses are double-stranded DNA viruses (~4 to 7 kb). They are known for causing tumors in the host it infects, and have previously been identified in a diverse array of organisms, including scorpions. The objective for this study was to identify known and novel viruses in scorpions. Using high-throughput sequencing and traditional molecular techniques we determine the genome sequences of cycloviruses and polyomaviruses. Sixteen of the forty-three scorpion samples were positive for eight different species of cycloviruses. According to ICTV guidelines, seven of the eight species were novel cycloviruses which were found in bark scorpions, stripe-tailed scorpions, yellow ground scorpions, and giant hairy scorpions (Centruroides sculpturatus, Paravaejovis spinigerus, Paravaejovis confusus & Hadrurus arizonensis) from Maricopa, Pinal, and Pima county in Arizona, USA. Additionally, one previously known cyclovirus species was recovered in bark scorpions (Centruroides sculpturatus) in Pima county which had previously been documented in guano from a Mexican free-tailed bat in Arizona. There were ten scorpions out of forty-three for which we recovered polyomavirus scorpion samples that grouped into four different polyomavirus species. Polyomaviruses were only identified in bark scorpions (Centruroides sculpturatus) from Maricopa, Pinal, and Pima county. Of the polyomavirus genomes recovered three belong to previously identified scorpion polyomavirus 1 and five to scorpion polyomavirus 3, and two represent two new species named scorpion polyomavirus 4 and scorpion polyomavirus 5. The implications of the discovery of cycloviruses and polyomaviruses from this study contributes to our understanding of viral diversity associated with Scorpions.
ContributorsNeil, Julia (Author) / Gomez, Magali (Co-author) / Varsani, Arvind (Thesis director) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Politics and Global Studies (Contributor)
Created2024-05
The Association Between Time to Eat and Students Fruit & Vegetable Consumption, Selection, and Waste
Description
Background: Studies have examined student fruit/vegetable (FV) consumption, selection, and waste related to lunch duration and found that longer duration at lunch was associated with greater consumption, selection, and reduced waste. However, few studies have investigated the relationship between time to eat and FVs. The aim of this research is to analyze the relationship between objective time to students took to eat (“time to eat”) as it relates to their fruit and vegetable consumption, selection, and plate waste.in elementary, middle, and high schools. Methods: A secondary analysis of cross-sectional study of 37 Arizona schools to discover the differences in the selection, consumption, and waste of FVs from students (Full N = 2226, Elementary N = 630, Middle School N = 699, High School N = 897) using objective time to eat measures. Zero-inflated negative binomial regressions examined differences in FV grams selected, consumed, and wasted adjusted for sociodemographics including race, ethnicity, eligibility for free or reduced lunch, academic year, and sex and clustering for students within schools. Results are presented across school level (elementary, middle, and high school).
Results: The average time taken to eat ranged from 10-12 minutes for all students. The association of time to eat and lunch duration were not closely related (r=0.03, p = 0.172). In the count model for every additional minute spent, there was a 0.5% greater likelihood of selecting FVs for elementary kids among those who took any FVs. In the zero-inflated model, it was found that there was a statistically significant relationship between time spent eating and the selection of fruits and vegetables. For the total sample and high schoolers, a minute more of eating time was associated with a 4.3% and 8.8% greater odds of selecting FV. This means that longer eating time increased the likelihood of choosing fruits and vegetables. The results indicated that the longer students took to eat, the higher the likelihood of consuming more of FVs. Each 10 more minutes spent eating (i.e., time to eat) is associated with a 5% increase in grams of FV selected relative to mean (for those that chose FV) over 1 week this equates to 32 g increase of FV selected. However, for middle schoolers, the time to eat was not found to be significant in relation to the grams of fruits and vegetables consumed. There was some significance in the sociodemographic factors such as gender (all) and other (middle school). There was a relationship between time taken to eat and waste as a proportion for fruits and vegetables. For example, among those among the students who wasted something (as a proportion of selection), each additional 10 minutes of eating time was associated with a .6% decrease in waste relative to the mean (for those who chose fruits and vegetables) over a week, resulting in a decrease in waste percentage of 16.5%. Among high schoolers, males had a slightly higher odds of wasting a proportion of fruits and vegetables.
Conclusions: This study aimed to examine the association between the time students take to eat during lunch and their fruit and vegetable (FV) consumption, selection, and plate waste. The findings revealed that the time to eat was related to FV consumption, depending on the school level. However, it was not significantly associated with FV selection or waste. The study emphasized the need for further research on time to eat, distinguishing it from the duration of lunch. Longer lunch periods and adequate time could influence better food choices, increased FV consumption, and reduced waste. The study highlighted the importance of interventions and school policies promoting healthier food choices and providing sufficient time for students to eat. Future research should validate these findings and explore the impact of socialization opportunities on promoting healthier eating habits. Understanding the relationship between lunch duration, time to eat, and students' dietary behaviors can contribute to improved health outcomes and inform effective strategies in school settings.
ContributorsDandridge, Christina Marie (Author) / Adams, Marc (Thesis advisor) / Whisner, Corrie (Committee member) / Bruening, Meg (Committee member) / Arizona State University (Publisher)
Created2023
Description
Precise modulation of gene expression is essential for proper tissue and cell-specific differentiation and function. Multiple distinct post-transcriptional regulatory mechanisms, such as miRNA (microRNA)-based regulation and alternative polyadenylation (APA), are an intrinsic part of this modulation and orchestrate intricate pathways to achieve and maintain balanced gene expression.MiRNA-based regulation and APA function through sequence motifs located in the 3’ Untranslated Region (3’UTR) of mRNA transcripts. MiRNAs are short (~22 nt) non-coding RNA molecules that bind target sequences within the 3’UTR of an mRNA transcript, inhibiting its translation or promoting its degradation. APA occurs during RNA transcription termination and leads to the preparation of mature mRNAs with different 3’UTR lengths, allowing shorter 3’UTRs to bypass miRNA regulation.
In addition to these two post-transcriptional forms of regulation, co-transcriptional mechanisms such as alternative RNA splicing, which produces distinct gene products from a precursor mRNA, are also important in controlling gene expression.
While miRNA-based regulation, APA, and alternative RNA splicing are important regulatory mechanisms, there is a lack of comprehensive understanding of how they interact and communicate with each other. This thesis studies these three forms of gene regulation in the nematode C. elegans, with the goal of extracting rules and mechanisms used by each of them in development to establish and maintain somatic tissue identity.
After isolating miRNA targets in multiple C. elegans somatic tissues, it was found that miRNAs can modulate the abundance of hnRNPs and SR proteins, which are known to control alternative RNA splicing in a dosage-dependent manner.To identify tissue-specific miRNAs, a nuclear fluorescent cell sorting (FACS)-based methodology named Nuc-Seq, was developed to isolate and sequence tissue-specific miRNAs from body muscle tissue. Nuc-Seq identified 2,848 muscle-specific protein-coding genes and 16 body muscle-specific miRNAs. This data was used to develop a high-quality body muscle-specific miRNA-APA Interactome which allows studies in regulatory processes in detail.
Taken together, this work highlights some of the complexity of pre- and post-transcriptional gene regulation and sheds light on how miRNA-based regulation, APA, and alternative RNA splicing are interconnected and are responsible for the establishment and maintenance of tissue identity.
ContributorsSchorr, Anna L (Author) / Mangone, Marco (Thesis advisor) / Harris, Robin (Committee member) / Sharma, Shalini (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2023
Description
Despite the prevalence of coyotes (Canis latrans) little is known about the viruses associated with this species. To assess the extent of viral research that has been conducted on coyotes, a literature review was performed. Over the last six decades, there have been many viruses that have been identified infecting coyotes. The pathology of some cases implies that infection is rare and lethal while others have been demonstrated to be endemic to coyotes. In addition, the majority of the prior analyses were done through serological assays that were limited to investigating target viruses. To help expand what is known about coyote-virus dynamics, viral assays were conducted on coyote scat. The samples were collected as part of transects established along the Salt River near Phoenix, Arizona, United States (USA). The recovered viral genomes were clustered with other deoxynucleic acid (DNA) viruses and analyzed to determine phylogeny and genetic identity. From the recovered viral genomes, there are two novel circoviruses, one novel naryavirus, five unclassified cressdnaviruses, and two previously identified species of anelloviruses from the Wawtorquevirus genus. For these viruses, new phylogenies for their groups and pairwise identity plots have been generated. These figures give insight into the potential hosts and the evolutionary history. In the case of the anelloviruses, they likely derived from a wood rat (Neotoma) host, given the anellovirus family’s host specificity and its similarity to another viral genome derived from a wood rat in Arizona, USA. Of the recovered circovirus genomes, one is associated with a viral isolate collected from a dust sample in Arizona, USA. The second circovirus species identified is within a clade that consists of rodent associated circoviruses and canine circovirus. Other recovered genomes expand clusters of unclassified cressdnaviruses. The recovered genomes support further genomic analysis. These findings help support the notion that there is a wealth of viral information to be identified from animals like coyotes. By understanding the viruses that coyotes are associated with, it is possible to better understand the viral impact on the urban environment, domesticated animals, and wildlife in general.
ContributorsHess, Savage Cree (Author) / Varsani, Arvind (Thesis advisor) / Kraberger, Simona (Committee member) / Upham, Nathan S (Committee member) / Arizona State University (Publisher)
Created2023
Description
Alpha herpesviruses are a family of neuroinvasive viruses that infect multiplevertebrate species. Alpha herpesviruses are responsible for human and livestock infections, most notably Herpes Simplex Virus (HSV), Varicella Zoster virus (VZV), and Pseudorabies Virus (PRV). PRV is a potent swine virus that can infect other mammals, and results in lethal encephalitis that can be devastating to livestock and of great financial expense to farmers. HSV, types 1 and 2, and VZV are widespread throughout the global human population, with estimates of the HSV-1 burden at about 60% of people worldwide. The hallmark of alpha herpesvirus infection is a persistent, lifelong infection that can reactivate throughout the lifespan of the host. Currently, the precise mechanisms of how these viruses undergo intracellular trafficking to emerge from the infected cell in epithelial tissues is not well understood. Many insights have been made with PRV in animal neurons, both in culture systems and animal models, about the viral genes and host factors involved in these processes. However, understanding of these mechanisms, and the interplay between viral and host proteins, in the human pathogen HSV-1 is even more lacking. Using recombinant fluorescent virus strains of HSV-1 and Total Internal Reflection Microscopy to image the transport of mature viral progeny in epithelial cells, it was determined that the egress of HSV-1 uses constitutive cellular secretory pathways. Specifically, the viral progeny traffic from the trans-Golgi network to the site of exocytosis at the plasma membrane via Rab6a secretory vesicles. This work will contribute to the understanding of how alpha herpesviruses complete their lifecycles in host cells, particularly at the sites where infection initially occurs and can spread to a new organism. Knowledge of these processes may lead to the development of therapeutics or prophylactics to reduce the burden of these viruses.
ContributorsBergeman, Melissa Hope (Author) / Hogue, Ian B (Thesis advisor) / Hogue, Brenda (Committee member) / Roberson, Robert (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2023
DescriptionA
ContributorsLund, Michael (Author) / Varsani, Arvind (Thesis advisor) / Upham, Nathan (Committee member) / Harris, Robin (Committee member) / Arizona State University (Publisher)
Created2023