Matching Items (281)
Description
Background
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
ContributorsZhang, Wenlu (Author) / Feng, Daming (Author) / Li, Rongjian (Author) / Chernikov, Andrey (Author) / Chrisochoides, Nikos (Author) / Osgood, Christopher (Author) / Konikoff, Charlotte (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ji, Shuiwang (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2013-12-28
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton Schools of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
Description
Coronaviruses are a significant group of viruses that cause enteric and respiratory infections in a variety of animals, including humans. Outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle Eastern Respiratory Syndrome (MERS) in the past 15 years has increased research into coronaviruses to gain an understanding of their structure and function so one day therapies and vaccines may be produced. These viruses have four main structural proteins: the spike, nucleocapsid, envelope, and membrane proteins. The envelope (E) protein is an integral membrane protein in the viral envelope that acts as a viroporin for transport of cations and plays an important role in pathogenesis and viral assembly. E contains a hydrophobic transmembrane domain with polar residues that is conserved across coronavirus species and may be significant to its function. This experiment looks at the possible role of one polar residue in assembly, the 15th residue glutamine, in the Mouse Hepatitis Virus (MHV) E protein. The glutamine 15 residue was mutated into positively charged residues lysine or arginine. Plasmids with these mutations were co-expressed with the membrane protein (M) gene to produce virus-like particles (VLPs). VLPs are produced when E and M are co-expressed together and model assembly of the coronavirus envelope, but they are not infectious as they do not contain the viral genome. Observing their production with the mutated E protein gives insight into the role the glutamine residue plays in assembly. The experiment showed that a changing glutamine 15 to positive charges does not appear to significantly affect the assembly of the VLPs, indicating that this specific residue may not have a large impact on viral assembly.
ContributorsHaller, Sarah S. (Author) / Hogue, Brenda (Thesis director) / Liu, Wei (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor) / Biodesign Institute (Contributor)
Created2017-05
Description
Globally, about two-thirds of the population is latently infected with herpes simplex virus type 1 (HSV-1). HSV-1 is a large double stranded DNA virus with a genome size of ~150kbp. Small defective genomes, which minimally contain an HSV-1 origin of replication and packaging signal, arise naturally via recombination during viral DNA replication. These small defective genomes can be mimicked by constructing a bacterial plasmid containing the HSV-1 origin of replication and packaging signal, transfecting these recombinant plasmids into mammalian cells, and infecting with a replicating helper virus. The absence of most viral genes in the amplicon vector allows large pieces of foreign DNA (up to 150kbp) to be incorporated. The HSV-1 amplicon is replicated and packaged by the helper virus to form HSV-1 particles containing the amplicon DNA. We constructed a novel HSV-1 amplicon vector system containing lambda phage-derived attR sites to facilitate insertion of transgenes by Invitrogen Gateway recombination. To demonstrate that the amplicon vectors work as expected, we packaged the vector constructs expressing Emerald GFP using the replication-competent helper viruses OK-14 or HSV-mScartlet-I-UL25 in Vero cells and demonstrate that the vector stock can subsequently transduce and express Emerald GFP. In further work, we will insert transgenes into the amplicon vector using Invitrogen Gateway recombination to study their functionality.
ContributorsVelarde, Kimberly (Author) / Hogue, Ian B (Thesis advisor) / Manfredsson, Fredric (Committee member) / Sandoval, Ivette (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2021
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
Scientists are entrusted with developing novel molecular strategies for effective prophylactic and therapeutic interventions. Antivirals are indispensable tools that can be targeted at viral domains directly or at cellular domains indirectly to obstruct viral infections and reduce pathogenicity. Despite their transformative potential in healthcare, to date, antivirals have been clinically approved to treat only 10 out of the greater than 200 known pathogenic human viruses. Additionally, as obligate intracellular parasites, many virus functions are intimately coupled with host cellular processes. As such, the development of a clinically relevant antiviral is challenged by the limited number of clear targets per virus and necessitates an extensive insight into these molecular processes. Compounding this challenge, many viral pathogens have evolved to evade effective antivirals. Therefore, a means to develop virus- or strain-specific antivirals without detailed insight into each idiosyncratic biochemical mechanism may aid in the development of antivirals against a larger swath of pathogens. Such an approach will tremendously benefit from having the specific molecular recognition of viral species as the lowest barrier. Here, I modify a nanobody (anti-green fluorescent protein) that specifically recognizes non-essential epitopes (glycoprotein M-pHluorin chimera) presented on the extra virion surface of a virus (Pseudorabies virus strain 486). The nanobody switches from having no inhibitory properties (tested up to 50 μM) to ∼3 nM IC50 in in vitro infectivity assays using porcine kidney (PK15) cells. The nanobody modifications use highly reliable bioconjugation to a three-dimensional wireframe deoxyribonucleic acid (DNA) origami scaffold. Mechanistic studies suggest that inhibition is mediated by the DNA origami scaffold bound to the virus particle, which obstructs the internalization of the viruses into cells, and that inhibition is enhanced by avidity resulting from multivalent virus and scaffold interactions. The assembled nanostructures demonstrate negligible cytotoxicity (<10 nM) and sufficient stability, further supporting their therapeutic potential. If translatable to other viral species and epitopes, this approach may open a new strategy that leverages existing infrastructures – monoclonal antibody development, phage display, and in vitro evolution - for rapidly developing novel antivirals in vivo.
ContributorsPradhan, Swechchha (Author) / Hariadi, Rizal (Thesis advisor) / Hogue, Ian (Committee member) / Varsani, Arvind (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2022
Description
Monkeypox virus (MPXV) is an orthopoxvirus that causes smallpox-like disease and has up to a 10% mortality rate, depending on the infectious strain. The global eradication of the smallpox virus has led to the decrease in smallpox vaccinations, which has led to a drastic increase in the number of human MPXV cases. MPXV has been named the most important orthopoxvirus to infect humans since the eradication of smallpox and has been the causative agent of the 2022 world-wide MPXV outbreak. Despite being highly pathogenic, MPXV contains a natural truncation at the N-terminus of its E3 homologue. Vaccinia virus (VACV) E3 protein has two domains: an N- terminus Z-form nucleic acid binding domain (Z-BD) and a C-terminus double stranded RNA binding domain (dsRBD). Both domains are required for pathogenesis, interferon (IFN) resistance, and protein kinase R (PKR) inhibition. The N-terminus is required for evasion of Z-DNA binding protein 1 (ZBP1)-dependent necroptosis. ZBP1 binding to Z- form deoxyribonucleic acid/ribonucleic acid (Z-DNA/RNA) leads to activation of receptor-interacting protein kinase 3 (RIPK3) leading to mixed lineage kinase domain- like (MLKL) phosphorylation, aggregation and cell death. This study investigated how different cell lines combat MPXV infection and how MPXV has evolved ways to circumvent the host response. MPXV is shown to inhibit necroptosis in L929 cells by degrading RIPK3 through the viral inducer of RIPK3 degradation (vIRD) and by inhibiting MLKL aggregation. Additionally, the data shows that IFN treatment efficiently inhibits MPXV replication in a ZBP1-, RIPK3-, and MLKL- dependent manner, but independent of necroptosis. Also, the data suggests that an IFN inducer with a pancaspase or proteasome inhibitor could potentially be a beneficial treatment against MPXV infections. Furthermore, it reveals a link between PKR and pathogen-induced necroptosis that has not been previously described.
ContributorsWilliams, Jacqueline (Author) / Jacobs, Bertram (Thesis advisor) / Langland, Jeffrey (Committee member) / Lake, Douglas (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2022
Description
Traditional public health strategies for assessing human behavior, exposure, and activity are considered resource-exhaustive, time-consuming, and expensive, warranting a need for alternative methods to enhance data acquisition and subsequent interventions. This dissertation critically evaluated the use of wastewater-based epidemiology (WBE) as an inclusive and non-invasive tool for conducting near real-time population health assessments. A rigorous literature review was performed to gauge the current landscape of WBE to monitor for biomarkers indicative of diet, as well as exposure to estrogen-mimicking endocrine disrupting (EED) chemicals via route of ingestion. Wastewater-derived measurements of phytoestrogens from August 2017 through July 2019 (n = 156 samples) in a small sewer catchment revealed seasonal patterns, with highest average per capita consumption rates in January through March of each year (2018: 7.0 ± 2.0 mg d-1; 2019: 8.2 ± 2.3 mg d-1) and statistically significant differences (p = 0.01) between fall and winter (3.4 ± 1.2 vs. 6.1 ± 2.9 mg d-1; p ≤ 0.01) and spring and summer (5.6 ± 2.1 vs. 3.4 ± 1.5 mg d-1; p ≤ 0.01). Additional investigations, including a human gut microbial composition analysis of community wastewater, were performed to support a methodological framework for future implementation of WBE to assess population-level dietary behavior. In response to the COVID-19 global pandemic, a high-frequency, high-resolution sample collection approach with public data sharing was implemented throughout the City of Tempe, Arizona, and analyzed for SARS-CoV-2 (E gene) from April 2020 through March 2021 (n = 1,556 samples). Results indicate early warning capability during the first wave (June 2020) compared to newly reported clinical cases (8.5 ± 2.1 days), later transitioning to a slight lagging indicator in December/January 2020-21 (-2.0 ± 1.4 days). A viral hotspot from within a larger catchment area was detected, prompting targeted interventions to successfully mitigate community spread; reinforcing the importance of sample collection within the sewer infrastructure. I conclude that by working in tandem with traditional approaches, WBE can enlighten a comprehensive understanding of population health, with methods and strategies implemented in this work recommended for future expansion to produce timely, actionable data in support of public health.
ContributorsBowes, Devin Ashley (Author) / Halden, Rolf U (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Conroy-Ben, Otakuye (Committee member) / Varsani, Arvind (Committee member) / Whisner, Corrie (Committee member) / Arizona State University (Publisher)
Created2022
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