Browsing by Subject "bioinformatics"
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Item Broadening the Definition of the Taxonomic Domain of Applicability of an Adverse Outcome Pathway Through Bioinformatics Approaches(2022-08) Jensen, MarissaFor the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single, or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and key event relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, which can be used to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence towards biological plausibility for the tDOA. Here, a case study describing the process of using bioinformatics to define the tDOA of an AOP is presented using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. While the AOP was developed to gain a particular biological understanding relative to Apis mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. This work demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species.Item Enhancing control of porcine rotavirus through the identification of candidate B cell epitopes(2020-08) Shepherd, FrancesFrom the moment piglets are born, their welfare is threatened by rotavirus (RV), a highly prevalent cause of acute diarrheal disease and mortality. Scientists and producers continue to grapple with how to improve vaccine and surveillance strategies to reduce infections. This ongoing challenge is due in part to a lack of information on which genetic changes within RV drive immune escape. The goals of this dissertation are twofold. We first aimed to investigate whether viral presence or detection in feces can be ameliorated by improved timing of prefarrow immunization. Our second aim was to elucidate B cell epitopes (BCEs) on the capsid proteins VP7 and VP4 to identify possible genetic drivers of vaccine immune escape and antigenic diversity. In Chapter 2, a longitudinal study on a commercial farm assessed whether the timing of prefarrow natural planned exposure (NPE) impacts the levels of RV detected in piglets’ feces. RV was continuously detected regardless of the number of NPE doses, and hypothesized that genetic changes at BCEs contribute to immune escape. We pursued this line of inquiry by elucidating BCEs with a bioinformatic approach. In Chapter 3, we validate and apply an in silico method to predict BCEs of RV VP7. In Chapter 4, we predict BCEs on the VP8*, the VP4 cleavage product that mediates host cell attachment. Alanine mutations at two predicted BCEs resulted in lower antisera binding titers, suggesting that the predicted sites were functional in antibody binding. This research provides evidence that computational approaches can yield immunologically-relevant information from RV sequence data alone and provides the first attempt at characterizing antigenic sites of RVB and RVC. Future surveillance efforts that focus on the predicted epitopes could help producers anticipate the accumulation of antigenic distance between vaccine and field strains, which will be crucial for improving vaccines and supporting piglet health.Item Estrogen Deficiency-Induced Phosphoproteomic Alterations In Skeletal Muscle Of Female Mice(2022-08) Peyton, MinaDynapenia, the age-related loss of muscle strength without the loss of muscle mass, significantly impacts the physical function and overall quality of life in older adults, thereby decreasing their health span. Skeletal muscle strength loss has been shown to occur earlier and is greater in aging females than males. Furthermore, clinical and preclinical studies have measured associations between skeletal muscle strength loss and the age at which circulating estrogen begins to decline in females. Despite copious years of skeletal muscle research, the molecular mechanisms underlying muscle strength loss in aging females remain poorly understood. Age-related protein phosphorylation changes have been reported in skeletal muscle of males, and protein phosphorylation alterations have been shown in cardiac muscle across age and sex. However, the extent and magnitude of these changes in the skeletal muscle phosphoproteome of females in response to estrogen deficiency have yet to be determined. This dissertation aims to further our molecular understanding of how estrogen deficiency impacts skeletal muscle function (i.e., the force-generating capacity of muscle) in females by investigating the skeletal muscle phosphoproteome using high-throughput mass spectrometry coupled with bioinformatic analyses and computational modeling. First, using an ovariectomy model, we determined the physiological remodeling of the skeletal muscle phosphoproteome associated with estrogen deficiency. Next, due to the controversies related to using an ovariectomy model to implicate estrogen-related changes in aging females and because the primary function of skeletal muscle is contraction (i.e., molecular force generation), we sought to discern estrogen deficiency-associated protein phosphorylation alterations in contracted skeletal muscle via evoked electrical stimulations in ovariectomized and natural aging ovarian-senescent female mice compared to their respective controls. Examining the phosphoproteomic alterations in resting, non-contracted, and contracted skeletal muscle of estrogen-deficient females, we identified novel phosphosites, candidate kinases and phosphatases, as well as illuminated key pathways that are sensitive to estrogen levels that may contribute to the loss of skeletal muscle strength. This dissertation provides new avenues for further research and novel targets for the development of therapeutics and interventions to mitigate the loss of skeletal muscle strength in females.Item Hitching a ride: A gastropod-associated microbiome community at a Hydrate Ride methane seep and impacts on local biogeochemical cycling(2022-10) Shaner, SydneyExploration of cold seeps from geological, chemical, and biological perspectives has grown exponentially in recent decades since the first discovery of cold seeps in the 1980s. Symbiotic relationships, often rooted in geochemistry of the environment, have proven to be ubiquitous at cold seeps. However, our understanding of symbiotic relationships at extreme environments is limited. In this thesis, we first review two kinds of cold seep systems—gas hydrate-forming seeps, using Hydrate Ridge as an example, and brine-influenced seeps, with a focus on the Gulf of Mexico—from geological, microbiological, and biogeochemical perspectives. We then report on the composition of microbial communities associated with provannid gastropods as characterized using 16S rRNA gene amplicon and clone libraries as well as Fluorescence In Situ Hybridization. The gastropod shells, collected from seeps at Hydrate Ridge and the Gulf of Mexico are covered with filamentous epibionts on their shells. Large filamentous epibionts were identified as Candidatus Marithrix, Thiomargarita nelsonii, and a previously undescribed Chloroflexi. Our analysis of three incomplete Chloroflexi’s genomes leads us to hypothesize that the Chloroflexi is an acetogen. Environmental samples from a previous sample revealed that the gastropod-associated community differed from the surrounding microbial communities, implying a selection mechanism for gastropod habitation and that the gastropod shell potentially serves as a unique niche. The diverse community of microbes on the shell of these seep-dwelling gastropods may represent a symbiotic relationship made possible by the gastropods motility that provides the attached microbial community with essential metabolites, while the attached community may serve the gastropod by providing it with a source of nutrition, and potentially detoxifying hydrogen sulfide.Item Mitochondrial mRNA termini processing in Trypanosoma brucei(2023-08) Smoniewski, ClaraA large and ever-expanding field, RNA biology is the study of the RNA lifecycle, how RNAs function, and their diverse roles in cellular processes. The most well-known RNA type are the protein-coding mRNAs transcribed from genes encoded in DNA. mRNAs progress through multiple steps during their lifecycle, one of which is maturation in which a 3' nonencoded nucleotide tail is added. These tails vary widely across organisms and organelles, both in composition and function. This dissertation examines the 3' tail addition and termini processing of mRNA transcripts in the mitochondrion of a parasitic protozoan Trypanosoma brucei. Trypanosomes have a single mitochondrion in which RNA regulation is crucial for gene expression changes necessary for host-switching. Although a working model for mitochondrial mRNA processing in T. brucei has been developed, transcript-specific gene regulation remains undefined. Differences in mRNA editing, stability, and translation remain unexplained, as do differences in 3' mRNA tail characteristics between transcripts and life stages. Here, I present several studies of the RNA lifecycle and mRNA termini processing in the mitochondrion of T. brucei. Chapter 1 contains an introduction to RNA, 3' mRNA tails, and trypanosomes. In Chapter 2, I explain our refinement of circTAIL-seq, a tool used to high-throughput sequence 3' and 5' termini. I define the circTAIL-seq error rate and describe a newly developed alignment protocol that allows for greater nuance in aligning reads. The discovery and characterization of circular mitochondrial mRNAs (circRNAs) is presented in Chapter 3. We show that circRNAs are present in both T. brucei life stages and are a subpopulation of total mRNAs with distinct characteristics. Chapter 4 contains a description of the effects of manipulating two poly(A) polymerase (PAP)-family proteins found in T. brucei’s mitochondria — KPAP1 and KPAP2. KPAP2 is found in unknown complexes of various sizes, and mutations of KPAP1 arginine methylation sites are shown to have transcript-specific effects on 3' tail characteristics. I then summarize my major conclusions and present a discussion of limitations and future directions of this work. Overall, this dissertation expands our understanding of the RNA lifecycle by further elucidating mitochondrial mRNA termini processing in T. brucei.Item Reciprocal Informants: Using Fungal Bioinformatics, Genomics, and Ecology to tie Mechanisms to Ecosystems(2019-08) Lofgren, LotusAcross both wild and human-structured ecosystems, fungi interact with every plant species on earth. From mycorrhizal mutualisms, harmless endophytes, and deadly pathogens, the results of these interactions can mean the difference between a plant’s ability to grow and flourish, or languish and expire. Fungal-host dynamics are not static traits, either over evolutionarily time or during the lifetime of individuals where ecological context dependency shapes the outcomes of fungal-host interactions. Understanding the ecological and genetic factors that structure plant-fungal relationships has wide ranging consequences for ecosystems, agro-ecosystems, and human health. However, it’s not well understood how complex genetic mechanisms and ecological pressures work in concert to structure the outcomes of fungal-host interactions, particularly among fungal mutualists. This dissertation contributes to this understanding by investigating how fungal-host relationships are regulated at two levels: broadly, investigating the ecology of fungal-host systems, and specifically, investigating the genetic and genomic basis of how these interactions are mediated. I begin Chapter 1 from the perspective of fungal ecology, investigating the influence of neighborhood (the surrounding plant community) on host specificity patterns using the host-specialist ectomycorrhizal (ECM) genus Suillus. The number of host species that a given fungal species will associate with, and how closely related these host species are, is the study of fungal host specificity. While some fungi associate with only a single species of host (high host specificity), most associate with tens or hundreds of host species (low host specificity). Fungi in the genus Suillus are famous for their high host specificity, primarily associating with plants in the family Pineaceae (particularly White Pines, Red Pines and Larchs). Using a combination of field sampling, sequencing, and colonization bioassays, I present evidence that one species, S. subaureus, has undergone a novel host-expansion onto Angiosperms, and argue that neighborhood effects influence ECM colonization outcomes over both space and time. In Chapter 2, I expand from fungal ecology into fungal genomes. Using genome mining and comparative genomics, I look for signatures of ECM host specificity using 19 genome sequenced Suillus species in relation to 1) other (non-Suillus) ECM fungi and 2) an intrageneric comparison between Suillus that specialize on Red Pine, White Pine or Larch. I present evidence for the involvement of several molecular classes in regulating Suillus host specificity including species specific small secreted proteins, G-protein coupled receptors, and terpene secondary metabolites. Finally, in Chapter 3, I use the genomic and bioinformatic tool sets developed in Chapters 1 and 2, to expand my analysis across the fungal phylogeny and ask questions about a potential molecular correlate of fungal guild and trophic mode: ribosomal DNA (rDNA) copy number. To do this, I developed a bioinformatic pipeline to estimate rDNA copy number variation from whole genome sequence data, and applied it to a phylogenetically and ecologically diverse set of 91 fungal genomes. I present evidence that rDNA copy number is inversely associated phylogenetic distance, but displays a high level of variation, spanning an order of magnitude in Suillus alone, with no detectable correlation to guild occupation or genome size. Taken together, the work presented here shows that genomic and bioinformatic approaches used in concert with classical ecological methodologies, offer great potential to expand our understanding of the two-way influence of ecosystem-level processes and gene-level mechanisms in structuring plant-fungal interactions.Item Use of Sequencing Technologies to Improve Swine Infectious Disease Management(2020-02) Tan, ShaoyuanThe swine industry is an indispensable part of the food production and agricultural system. However, infectious disease poses great threats to the industry. The current situation is that “old” infectious diseases are not totally under control and “new” pathogens keep emerging. In addition, via food chain and direct or indirect contact, some swine pathogens can infect humans and antimicrobial resistance arising from swine pathogens can also adversely impact public health. The threat of infectious disease to the swine population has been further magnified by globalization which increases the rate and breadth of disease transmission, thus having a more devastating impact. Fortunately, scientific advances have greatly bolstered our ability to develop effective disease control strategies. Sequencing technology has emerged as a powerful solution to deal with the challenging infectious disease situations we are facing today. The advantages of sequencing as a diagnostic tool are numerous. From our research, we confirmed that sequencing has improved the disease diagnostic resolution to the strain level, providing more precise and effective control strategies; it is able to generate additional genomic information for functional prediction of infectious agents, such as antimicrobial resistance profiling; and sequencing can facilitate a prompt response against emerging eventualities due to its ability to rapidly detect pathogens in a sample, including the novel or unexpected ones. Going forward, the more frequent use of sequencing in swine medicine can enhance our ability to predict and control the emergence and transmission of infectious disease within swine populations.Item Variants from "The role of deleterious substitutions in crop genomes"(2016-07-26) Kono, Thomas J Y; Fu, Fengli; Mohammadi, Mohsen; Hoffman, Paul J; Liu, Chaochih; Stupar, Robert M; Smith, Kevin P; Tiffin, Peter; Fay, Justin C; Morrell, Peter L; konox006@umn.edu; Kono, Thomas J YSNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.