Browsing by Subject "mutagenesis"

Now showing 1 - 4 of 4
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    Efficiently Storing and Discovering Knowledge in Databases via Inductive Logic Programming Implemented Directly in Databases
    (2015-07) Repaka, Ravikanth
    Inductive Logic Programming (ILP) uses inductive, statistical techniques to generate hypotheses which incorporate the given background knowledge to induce concepts that cover most of the positive examples and few of the negative examples. ILP uses techniques from both logic programming and machine learning. Research has been evolving from several years in this field and many systems are developed to solve ILP problems and most of these systems are developed in Prolog and take the input in the form of text files or other similar formats. This thesis proposes to use a relational database to store background knowledge, positive and negative examples in the form of database entities. This information is then manipulated directly uses ILP techniques efficiently in the process of generating hypotheses. The database does the heavy lifting by efficiently handling and storing a very large number of intermediate rules which are generated in the process of finding the required hypotheses. The proposed system will be helpful to generate hypotheses from relational databases. The system also provides a mechanism to store the given data into a database which exists in text files. Sequential covering algorithm is used to find the hypotheses which cover all positive examples and few or none of the negative examples. The proposed system is tested on real world datasets, Mutagenesis and Chess Endgame, and the generated hypotheses and its accuracy are similar to the results of existing systems which were tested on the same datasets. The results are promising and this encourages researchers to use the system in future to discover the knowledge for other datasets or in relational databases.
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    Overlapping functions of APOBEC enzymes in antiviral immunity and cancer
    (2017-07) Starrett, Gabriel
    APOBEC enzymes are a family of innate antiviral enzymes that form an important barrier against DNA-based pathogens. Encoding and expressing these DNA mutating enzymes, however, is an inherently risky endeavor for the stability of the host genome if not regulated appropriately. These risks have been demonstrated in numerous cancers where APOBEC3B is overexpressed and the APOBEC-associated mutation signature is enriched. Emphasizing the importance of this observation, elevated expression of APOBEC3B and presence of APOBEC-associated mutations has now been consistently linked to aggressive phenotypes and worse outcome in cancer patients. Here I present data demonstrating overlapping functions of APOBEC3 enzymes in antiviral immunity and cancer. In both of these models, APOBEC3 enzymes contribute potentially deleterious and beneficial mutations potentially impacting the survival of tumors and viruses. Additionally, the functions of these enzymes can be modulated by heritable germline mutations in the APOBEC3 locus and viral infections. DNA viruses can also act as valuable molecular probes into the regulation of APOBEC3 enzymes in tumors leading to the development of better therapies.
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    Studies of the mutagenesis and virus-host interactions of hepadnaviruses and retroviruses
    (2021-11) McDaniel, Yumeng
    Although viral infection is preventable by vaccination and antiviral treatments are available, up to 1 million people die every year from hepatitis B virus (HBV)-associated liver diseases. In line with this notion, there is an effective vaccine available for feline leukemia virus (FeLV), but FeLV remains a common infection among domesticated cat populations and accounts for many clinical syndromes that typically end with death within 1 to 3 years after the initial diagnosis. Therefore, the need for new antiviral agents for treating human and veterinary viral pathogens exists, even in instances where effective vaccines are available. Reverse transcriptase (RT) is an essential enzyme for the replication life cycle of both retroviruses (i.e., human immunodeficiency virus type 1, HIV-1) and hepadnaviruses (i.e., HBV). Previous studies have shown two types of small molecules possessing anti-HIV-1 activity, mainly through targeting reverse transcriptase (RT) and the reverse transcription pathway - namely viral mutagens (i.e., decitabine, 5-azacytidine and KP1212) and ribonucleotide reductase inhibitors (RNRIs) (i.e., gemcitabine and resveratrol). Our research group has shown that decitabine and gemcitabine can also inhibit FeLV and murine leukemia viruses (MuLV) replication, which are closely related gammaretroviruses. Based upon these observations, Part 1 of this dissertation sought to test following two hypotheses: 1) mutagen and RNRI or the combination of a mutagen and an RNRI will possess potent anti-HBV activity; and 2) distinct antiviral mechanisms can be elicited by a viral mutagen. A family of host proteins, i.e., human apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3, A3) proteins, can induce viral mutagenesis, and therefore act as a cellular-based viral mutagen. APOBEC3 family member proteins can deaminate cytosines in single-strand (ss) DNA, which restricts HIV-1, retrotransposons, and other viruses such as HBV, but can cause a mutator phenotype in many cancers. Part 2 of this dissertation sought to characterize the deamination hotspots of APOBEC3 proteins, and to test the hypothesis that deamination hotspots among APOBEC3 family members are defined by both target site sequence and ssDNA structure. Although anti-HBV therapeutic discovery targeting host factors and screening for inhibitors are in progress, there is a significant knowledge gap regarding HBV-host cell interaction. This line of research investigation is critical to public health as HBV infection accounts for 54% of all hepatocellular carcinomas (HCCs), which is notable as it is the second highest cause of cancer-related mortality worldwide. An enhanced understanding of HBV-host cell interactions will help to improve general knowledge of HBV biology, identify potential targets for antiviral intervention to prevent HCC, and provide insights that could prove useful in the early diagnosis of HCC and the discovery of HCC-targeted therapeutics. Part 3 of this dissertation describes the results of an analysis of HBV-infected cells for testing the hypothesis that host genes involved in the cellular antiviral response and HCC development can be identified by transcriptome analysis. Together, the studies conducted in this dissertation serve to lay the foundation for future basic and translational research studies.
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    Studies on the Molecular Determinants of Human Retrovirus Diversity
    (2021-09) Meissner, Morgan
    The human immunodeficiency viruses (HIVs) are two species (HIV type 1, HIV-1; HIV type 2, HIV-2) in the Lentivirus genus of the Retroviridae family of viruses and are the etiological agents of acquired immunodeficiency syndrome (AIDS). Nearly 75 million people have been infected with HIV-1 and HIV-2 since their emergence in the human population and they are responsible for the deaths of almost 32 million individuals to date. One of the key drivers of the HIV-1 pandemic is the extreme genetic diversity of the virus, which drives the development of antiviral drug resistance and frustrates vaccine development. Retroviruses also exhibit considerable structural diversity, which may have important implications for infectivity and replication. Human T-cell leukemia virus type 1 (HTLV-1), within the Deltaretrovirus genus, is also a major pathogenic human retrovirus. HIV-2 and HTLV-1 exhibit markedly reduced rates of transmissibility and potentially evolution compared with HIV-1 and are therefore understudied relative to their pandemic counterpart. The overarching goal of this thesis was to characterize the viral and cellular determinants of the molecular diversity of human retroviruses, with an emphasis on HTLV-1 and HIV-2. To this end, experiments were conducted which 1) characterized the structural diversity of authentic HTLV-1 particles derived from the chronically infected SP cell line, demonstrating that intact capsid cores are relatively rare among HTLV-1 particles; and 2) examined the contribution of host apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins to HIV-2 mutagenesis, which revealed that despite their role as potent mutagens of HIV-1, APOBEC3-mediated mutagenesis of HIV-2 is limited. Additionally, a user-friendly sequence analysis workflow was developed that enables the ultra-accurate detection of mutations within HIV-1 and HIV-2, which reduces the background error rate of traditional Illumina next-generation sequencing by approximately 100-fold. This workflow is already being employed to characterize the contributions of additional cellular proteins to retroviral mutagenesis, including the host protein SAM domain and HD domain- containing protein 1 (SAMHD1). Taken together, these studies provide new insights into the structural and genetic diversity of human retroviruses, particularly those which have historically been poorly characterized and underappreciated.