Matching Items (42)
Description
The goal of this project was to design and create a genetic construct that would allow for <br/>tumor growth to be induced in the center of the wing imaginal disc of Drosophila larvae, the <br/>R85E08 domain, using a heat shock. The resulting transgene would be combined with other <br/>transgenes in a single fly that would allow for simultaneous expression of the oncogene and, in <br/>the surrounding cells, other genes of interest. This system would help establish Drosophila as a <br/>more versatile and reliable model organism for cancer research. Furthermore, pilot studies were <br/>performed, using elements of the final proposed system, to determine if tumor growth is possible <br/>in the center of the disc, which oncogene produces the best results, and if oncogene expression <br/>induced later in development causes tumor growth. Three different candidate genes were <br/>investigated: RasV12, PvrACT, and Avli.
ContributorsSt Peter, John Daniel (Author) / Harris, Rob (Thesis director) / Varsani, Arvind (Committee member) / School of Molecular Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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
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
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
Caracals (Caracal caracal) are a felid species native to regions of southern Africa and western and central Asia. Despite their relatively high prevalence, the majority of research conducted on caracals has been undertaken on captive individuals, which encounter significantly different environments and exhibit different behaviors in comparison to caracals in the wild. Thereby, they likely have a vastly different virome. The goal of this study was to identify known and unknown DNA viruses associated with free-ranging caracals. Caracal fecal and organ samples were obtained from a caracal surveillance study undertaken in the Western Cape region of South Africa. Parasitic ticks found feeding on caracals were also obtained. Using a viral metagenomic informed approach, a novel circovirus (family Circoviridae) was detected and characterized in caracal fecal, kidney, spleen, and liver samples, as well as in ticks feeding on the caracals. To our knowledge, this is the first circovirus identified in caracals. The novel circovirus was determined to be closely related to a canine circovirus. These findings expand the knowledge of viral diversity and caracals and are greatly important to caracal conservation efforts as well as conservation efforts of other animals within their ecosystem.
ContributorsCollins, Courtney (Author) / Varsani, Arvind (Thesis director) / Dolby, Greer (Committee member) / Kraberger, Simona (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2022-05
Description
Members of the Delphinidae family are widely distributed across the world’s oceans. We used a viral metagenomic approach to identify viruses in orca (Orcinus orca) and short-finned pilot whale (Globicephala macrorhynchus) muscle, kidney, and liver samples from deceased animals. From orca tissue samples (muscle, kidney, and liver), we identified a novel polyomavirus (Polyomaviridae), three cressdnaviruses, and two genomoviruses (Genomoviridae). In the short-finned pilot whale we were able to identify one genomovirus in a kidney sample. The presence of unclassified cressdnavirus within two samples (muscle and kidney) of the same animal supports the possibility these viruses might be widespread within the animal. The orca polyomavirus identified here is the first of its species and is not closely related to the only other dolphin polyomavirus previously discovered. The identification and verification of these viruses expands the current knowledge of viruses that are associated with the Delphinidae family.
ContributorsSmith, Kendal Ryan (Author) / Varsani, Arvind (Thesis director) / Kraberger, Simona (Committee member) / Dolby, Greer (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Arachnids belong to the phylum Arthropoda, the largest phylum in the animal kingdom. Ticks are blood-feeding arachnids that vector numerous pathogens of significant medical and veterinary importance, while scorpions have become a common concern in urban desert cities due to the high level of toxicity in their venom. To date, viruses associated with arachnids have been under sampled and understudied. Here viral metagenomics was used to explore the diversity of viruses present in ticks and scorpions. American dog ticks (Dermacentor variabilis) and blacklegged ticks (Ixodes scapularis) were collected in Pennsylvania while one hairy scorpion (Hadrurus arizonensis) and four bark scorpions (Centruroides sculpturatus) were collected in Phoenix. Novel viral genomes described here belong to the families Polyomaviridae, Anelloviridae, Genomoviridae, and a newly proposed family, Arthropolviridae.
Polyomaviruses are non-enveloped viruses with a small, circular double-stranded DNA (dsDNA) genomes that have been identified in a variety of mammals, birds and fish and are known to cause various diseases. Arthropolviridae is a proposed family of circular, large tumor antigen encoding dsDNA viruses that have a unidirectional genome organization. Genomoviruses and anelloviruses are ssDNA viruses that have circular genomes ranging in size from 2–2.4 kb and 2.1–3.8 kb, respectively. Genomoviruses are ubiquitous in the environment, having been identified in a wide range of animal, plant and environmental samples, while anelloviruses have been associated with a plethora of animals.
Here, 16 novel viruses are reported that span four viral families. Eight novel polyomaviruses were recovered from bark scorpions, three arthropolviruses were recovered from dog ticks and one arthropolvirus from a hairy scorpion. Viruses belonging to the families Polyomaviridae and Arthropolviridae are highly divergent. This is the first more extensive study of these viruses in arachnids. Three genomoviruses were recovered from both dog and deer ticks and one anellovirus was recovered from deer ticks, which are the first records of these viruses being recovered from ticks. This work highlights the diversity of dsDNA and ssDNA viruses in the arachnid population and emphasizes the importance of performing viral surveys on these populations.
Polyomaviruses are non-enveloped viruses with a small, circular double-stranded DNA (dsDNA) genomes that have been identified in a variety of mammals, birds and fish and are known to cause various diseases. Arthropolviridae is a proposed family of circular, large tumor antigen encoding dsDNA viruses that have a unidirectional genome organization. Genomoviruses and anelloviruses are ssDNA viruses that have circular genomes ranging in size from 2–2.4 kb and 2.1–3.8 kb, respectively. Genomoviruses are ubiquitous in the environment, having been identified in a wide range of animal, plant and environmental samples, while anelloviruses have been associated with a plethora of animals.
Here, 16 novel viruses are reported that span four viral families. Eight novel polyomaviruses were recovered from bark scorpions, three arthropolviruses were recovered from dog ticks and one arthropolvirus from a hairy scorpion. Viruses belonging to the families Polyomaviridae and Arthropolviridae are highly divergent. This is the first more extensive study of these viruses in arachnids. Three genomoviruses were recovered from both dog and deer ticks and one anellovirus was recovered from deer ticks, which are the first records of these viruses being recovered from ticks. This work highlights the diversity of dsDNA and ssDNA viruses in the arachnid population and emphasizes the importance of performing viral surveys on these populations.
ContributorsSchmidlin, Kara (Author) / Varsani, Arvind (Thesis advisor) / Van Doorslaer, Koenraad (Committee member) / Stenglein, Mark (Committee member) / Arizona State University (Publisher)
Created2019
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
Genetic Ablation Systems of the Drosophila Imaginal Wing Disc: Building and Testing the TASER System
Description
Drosophila melanogaster, commonly known as the fruit fly, is widely used in genetic research due to its ease of genetic manipulation and well characterized genome. One of its structures, the imaginal wing disc, has played a key role in uncovering the mechanisms underlying tissue regeneration. Damage is typically induced via physical, irradiation, or genetic ablation to study these regenerative processes. Recently, genetic techniques have been developed to cause targeted damage in situ by triggering cell death through the expression of pro-apoptotic or necrotic genes. The GAL4/UAS system allows for precise, tissue-specific cell death by the induction of a heat shift, an exposure of a higher temperature for an extended period of time. However, this 1st system is unable to express genes of interest in the wing disc to determine how other factors influence the regenerative process. Therefore, another approach was created, known as DUAL (Duration and Location) control, to allow the induction of both cell death as well as gene expression in the surrounding cells. The DUAL control system is regulated with exposure to higher temperature for a shorter period, referred to as a heat shock. The limitation of this 2nd system is its inability to temporally separate the timing of cell death from gene expression. This lack of control over timing highlights the need for a newer ablation system. In this work, we chose to create a novel system, termed the Temporal Ablation with Separation of Expression Regulation (TASER) system. The TASER system uses both heat shift and heat shock to provide refined control over the timing of cell ablation and gene expression. The system was developed by crossing specific Drosophila stocks that include genetic components like GAL80ts and GAL4tp, allowing for differing temporal regulation. We confirmed that the system is functional at separating the gene expression from ablation when the heat shock precedes the heat shift. However, initiating the heat shift first led to not only ablation, but also premature gene expression due to prolonged high temperatures. Despite this drawback, the TASER system holds significant potential in providing a more precise temporal control in regeneration studies, making it a valuable tool for future research.
ContributorsRogler, Isabel (Author) / Harris, Rob (Thesis director) / Bean, Heather (Committee member) / Huijben, Silvie (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / School of International Letters and Cultures (Contributor)
Created2024-12