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Full-Text Articles in Life Sciences
Unraveling Plant-Microbe-Microbe Interactions: Host And Microbial Colonization Determinants Across Experimental Scales, Bridget O'Banion
Unraveling Plant-Microbe-Microbe Interactions: Host And Microbial Colonization Determinants Across Experimental Scales, Bridget O'Banion
Doctoral Dissertations
Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host and microbial mechanisms are likely important mediators of interactions. We combine information from large-scale datasets across diverse plant hosts with experimental genetic manipulation assays in model Arabidopsis seedlings to converge on a conserved role for metabolite production and transport in mediating host-microbe interactions. Applying a diverse set of analytical tools to microbial communities at various complexity levels will advance our knowledge of the scalability of observed phenotypes and, ultimately, help to decipher the mechanisms dictating plant–microbe interactions …
Accurate Simulation Of Reads And Improved Strategies For Abundance Estimation Supporting Reduced Representation Sequencing For Metagenomics, Ryan Kuster
Doctoral Dissertations
Next generation sequencing has impacted all areas of biology by providing affordable investigations into some of the most complex processes underpinning life. With its ubiquitous application, there is still benefit in considering the nuances of the technology and its downstream analysis. Sequencing libraries produced by fragmenting DNA with restriction enzyme digests limit the scope of sequencing to a reduced set of genomic loci, allowing for deeper sequencing of those regions at a reduced cost per sample. These sequencing libraries have been used to determine genetic markers within populations of closely related individuals due to their sensitivity and preservation within populations. …
Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones
Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones
Doctoral Dissertations
Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …
The Effects Of Urbanization On The Avian Gut Microbiome, Mae Berlow
The Effects Of Urbanization On The Avian Gut Microbiome, Mae Berlow
Doctoral Dissertations
The gut microbiome influences and is influenced by the host, and can affect the host organism by contributing to health, development and immunity. Similarly, the host can influence this community; it’s makeup can vary with host species, locality, diet, social stressors, and environmental stressors. Some of these environmental stressors have arisen due to human-induced rapid environmental change, like urbanization. The physiology and behaviors of organisms that are able to persist in urban environments are often different from their non-urban congeners. Nutrition, development, and immunity—all of which are affected by the gut microbiome—are important factors that can determine survival in urban …
More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia
More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia
Doctoral Dissertations
This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member …
Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz
Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz
Doctoral Dissertations
A diverse community of bacteria populates the mammalian gastrointestinal tract. These populations exist in a balance with the host assisting with key functions, particularly metabolism of intractable fibers and immune modulation. Disruption of this balance can lead to diseases such as infection, inflammatory bowel syndrome, and obesity. Common symptoms include chronic pain, chronic inflammation, and altered metabolism. Several taxonomic classifications of bacteria have been associated with these diseases, but Recent studies have indicated that these finding are not always statistically valid. An explanation for this is that microbial communities between individuals and even across time can vary substantially even when …