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Articles 1 - 30 of 52
Full-Text Articles in Life Sciences
A Temporal Analysis Of The Microbiota And Biofouling Development On Artificial Substrates In The Port Everglades Inlet, Florida, Denise Swack
All HCAS Student Capstones, Theses, and Dissertations
A pilot project was deployed in Port Everglades Inlet, Florida that aimed to evaluate the biofilm composing the microbiome on ecologically engineered artificial substrates used to build Coastal Marine Infrastructure. In April of 2017, an Articulated Concrete Block Mattress comprised of an ecological engineered concrete substrate and a standard smooth surface control substrates were compared. This study will provide a profile on the microbiome community on artificial substrates within Port Everglades Inlet on bio-enhancing concrete-based solutions in our Coastal Marine Infrastructure. To study the microbial community, the 16s rRNA technology was used in Illumina’s high-throughput DNA sequencing. Samples were collected …
From Microbes To Management: Spatial And Temporal Variations In Available Vegetation Affect The Gut Microbiota In A Population Of Free-Ranging Generalist Herbivores, Olivia K. Rodríguez
From Microbes To Management: Spatial And Temporal Variations In Available Vegetation Affect The Gut Microbiota In A Population Of Free-Ranging Generalist Herbivores, Olivia K. Rodríguez
Boise State University Theses and Dissertations
The effects of extrinsic environmental factors that shape ecological systems are not only seen at the macroscopic level, but additionally influence and govern the host-associated microbial communities of their mammalian hosts. These microbial communities are susceptible to the fluctuation of abiotic and biotic factors which affect their host organisms. The surge in the research of microbiota–communities of archaea, bacteria, fungi, and viruses residing in various environmental systems–has shown that these communities can profoundly influence animal health. As such, monitoring microbiota has allowed for a new approach to study animal health and physiology. This is of particular benefit in the conservation …
Trained Immunity Enhances The Immune Response And Maintains Microbiome Diversity In Aging And Sepsis, P. Spencer Gill
Trained Immunity Enhances The Immune Response And Maintains Microbiome Diversity In Aging And Sepsis, P. Spencer Gill
Electronic Theses and Dissertations
The global population is rapidly aging. It is estimated that over the next thirty years, the number of individuals >60 years of age will increase by over a billion, and the number of individuals over age 80 may increase by 300 million. As humans age, our immune system becomes progressively weaker through a process called immune senescence. This age-related decrease in immune function increases susceptibility to infection and chronic diseases. Sepsis is a leading cause of death worldwide. Over the past two decades, there has been an increased incidence of sepsis which is due, in part, to our aging population …
The Brown Bear Gut Microbiome: A Novel Tool For Conservation & Management, Sarah M. Trujillo
The Brown Bear Gut Microbiome: A Novel Tool For Conservation & Management, Sarah M. Trujillo
All NMU Master's Theses
Gut microbiomes (GMBs), complex communities of microorganisms inhabiting the gastrointestinal tracts of their hosts, perform countless micro-ecosystem services such as facilitating energy uptake and modulating immune responses. While scientists increasingly recognize the role GMBs play in host health, the role of GMBs in wildlife ecology and conservation has yet to be realized fully. Here, I use brown bears (Ursus arctos) as an ecological model to investigate (1) how both extrinsic and intrinsic factors influence GMB community membership and structure; and (2) the correlation between GMB membership and brown bear health metrics. To achieve these aims, I subsampled archived …
Considerations And Best Practices In Animal Science 16s Ribosomal Rna Gene Sequencing Microbiome Studies, Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock Jr, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramírez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Considerations And Best Practices In Animal Science 16s Ribosomal Rna Gene Sequencing Microbiome Studies, Margaret D. Weinroth, Aeriel D. Belk, Chris Dean, Noelle Noyes, Dana K. Dittoe, Michael J. Rothrock Jr, Steven C. Ricke, Phillip R. Myer, Madison T. Henniger, Gustavo A. Ramírez, Brian B. Oakley, Katie Lynn Summers, Asha M. Miles, Taylor B. Ault-Seay, Zhongtang Yu, Jessica L. Metcalf, James E. Wells
Roman L. Hruska U.S. Meat Animal Research Center: Reports
Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology, microbiology, microbial ecology, computer science, and bioinformatics—in addition to the traditional considerations when conducting an animal science study—makes microbiome studies sometimes intimidating due to the intersection of different fields. The objective of this review is to serve as a jumping-off point for those animal scientists less familiar with 16S rRNA gene sequencing and analyses and to bring up common issues and concerns that arise …
Spotted Salamander Egg Masses Exhibit A Unique Internal Microbiome In Relation To Their Environment, Elizabeth Leonard
Spotted Salamander Egg Masses Exhibit A Unique Internal Microbiome In Relation To Their Environment, Elizabeth Leonard
Senior Honors Theses
Microbial studies have led to various ecological and medicinal discoveries. Amphibian eggs, like those of Ambystoma maculatum, exhibit natural resistance to bacterial invasion that may be microbiome related. The purpose of this research was to sequence the external and internal microbiome of A. maculatum egg masses and compare with the environmental microbiome. It was hypothesized that the external and internal microbiome would bear more similarity to each other than the water. A significant difference was observed between the microbiome of the inside surface of the egg mass and the water but not the outside surface of the egg and …
Developing Inside A Layer Of Germs—A Potential Role For Multiciliated Surface Cells In Vertebrate Embryos, Ryan R. Kerney
Developing Inside A Layer Of Germs—A Potential Role For Multiciliated Surface Cells In Vertebrate Embryos, Ryan R. Kerney
Biology Faculty Publications
This paper reviews current research on the microbial life that surrounds vertebrate embryos. Several clades are believed to develop inside sterile—or near-sterile—embryonic microhabitats, while others thrive within a veritable zoo of microbial life. The occurrence of embryo-associated microbes in some groups, but not others, is an under-appreciated transition (possibly transitions) in vertebrate evolution. A lack of comparable studies makes it currently impossible to correlate embryo-associated microbiomes with other aspects of vertebrate evolution. However, there are embryonic features that should instruct a more targeted survey. This paper concludes with a hypothesis for the role of multiciliated surface cells in amphibian and …
Catechin And Other Catechol-Containing Secondary Metabolites: Bacterial Biotransformation And Regulation Of Carbohydrate Metabolism, Sara Knezevic, Asma Ghafoor, Samaneh Mehri, Ali Barazi, Maksymilian Dziura, John F. Trant, Christopher A. Dieni
Catechin And Other Catechol-Containing Secondary Metabolites: Bacterial Biotransformation And Regulation Of Carbohydrate Metabolism, Sara Knezevic, Asma Ghafoor, Samaneh Mehri, Ali Barazi, Maksymilian Dziura, John F. Trant, Christopher A. Dieni
Chemistry and Biochemistry Publications
Background: Catechol, 1,2-dihydroxybenzene, prepared through bacterial biotransformation from higher order polyphenols, has been proposed to regulate carbohydrate metabolism, especially in the context of type 2 diabetes. This review aims to contextualize this finding. It describes the bacterial biosynthesis of catechol both from glucose, and as a degradation product of higher order natural products through bacterial transformation. The review then considers the mechanism of action of glycemic-regulating catechol-containing materials and the complications arising from balancing their inherent activity with that of catechol, their common degradation product. It then enumerates potential dietary sources of catechin from common foods. Methods: Articles were found …
Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos
Factors Influencing Primate Hair Microbiome Diversity, Catherine Kitrinos
Masters Theses
Primate hair is both a substrate upon which essential social interactions occur and an important host-pathogen interface. As commensal microbes provide important immune functions for their hosts, understanding the microbial diversity in primate hair could provide insight into primate immunity and disease transmission. While studies of human hair and skin microbiomes show differences in microbial communities across body regions, little is known about the nonhuman primate hair microbiome. In this study, we collected hair samples (n=159) from 8 body regions across 12 nonhuman primate species housed at 3 US institutions to examine 1) the diversity and composition of the primate …
Dietary And Pharmacologic Manipulations Of Host Lipids And Their Interaction With The Gut Microbiome In Non-Human Primates, Jennifer M. Lang, Leslie R. Sedgeman, Lei Cai, Joseph D. Layne, Zhen Wang, Calvin Pan, Richard Lee, Ryan E. Temel, Aldons J. Lusis
Dietary And Pharmacologic Manipulations Of Host Lipids And Their Interaction With The Gut Microbiome In Non-Human Primates, Jennifer M. Lang, Leslie R. Sedgeman, Lei Cai, Joseph D. Layne, Zhen Wang, Calvin Pan, Richard Lee, Ryan E. Temel, Aldons J. Lusis
Physiology Faculty Publications
The gut microbiome influences nutrient processing as well as host physiology. Plasma lipid levels have been associated with the microbiome, although the underlying mechanisms are largely unknown, and the effects of dietary lipids on the gut microbiome in humans are not well-studied. We used a compilation of four studies utilizing non-human primates (Chlorocebus aethiops and Macaca fascicularis) with treatments that manipulated plasma lipid levels using dietary and pharmacological techniques, and characterized the microbiome using 16S rDNA. High-fat diets significantly reduced alpha diversity (Shannon) and the Firmicutes/Bacteroidetes ratio compared to chow diets, even when the diets had different compositions …
Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan
Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan
Biology Theses
Fungus-growing ants (Attini: Formicidae) and their fungal cultivars participate in ant-fungus mutualism that share a 50-million-year-old coevolutionary history. Fungal cultures are grown in gardens alongside ants and a diverse collection of microbes that interact with both species in mutualistic, commensal, and antagonistic relationships. These microbes aid in digestion and detoxification of food, provide essential nutrients, help in nest hygiene, and play a dominant role in defense against pathogens and disease. Microbial communities of many model species have been shown to change in a laboratory setting as compared to their natural environment. High-throughput 16s sequencing of the V4 variable region was …
You Are What You Eat — Exploring The Microbiome Through Inquiry-Based Labs. Microbiome Lesson Plans, Karla S. Fuller
You Are What You Eat — Exploring The Microbiome Through Inquiry-Based Labs. Microbiome Lesson Plans, Karla S. Fuller
Open Educational Resources
If these commonly used spices have the ability to inhibit pathogenic bacterial growth, could they also potentially inhibit the growth of normal, harmless bacteria that live in your body? In this lab, we will test common bacteria for resistance to food additives.
Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells
Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells
Master's Theses
The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …
Neuroinflammation, Peripheral Inflammation And Gut Microbiome Profiles In Male Mice From Two Proposed Mouse Models Of Social Behavior Deficits, Sarah Parkinson
Neuroinflammation, Peripheral Inflammation And Gut Microbiome Profiles In Male Mice From Two Proposed Mouse Models Of Social Behavior Deficits, Sarah Parkinson
Electronic Theses and Dissertations
Autism spectrum disorder (ASD) is a neurodevelopmental disorder marked by social deficits and repetitive actions. A communication pathway exists between the brain and gut called the gut-brain axis. It is thought that gut bacteria can secrete signaling molecules, triggering inflammation across the body. These studies attempt to determine if markers are expressed in two mouse models of ASD behaviors, BTBR and a valproic acid model. Immunohistochemistry of ionized calcium binding adaptor molecule 1 from male mouse brain tissue showed no microglial activation in any group. Cytokine analysis did exhibit an increase in interleukin 1 (IL-1) in male adult mice only. …
Exploring Microbiome Functional Dynamics Through Space And Time With Trait-Based Theory, Leonora S. Bittleston, Jessica R. Bernardin
Exploring Microbiome Functional Dynamics Through Space And Time With Trait-Based Theory, Leonora S. Bittleston, Jessica R. Bernardin
Biology Faculty Publications and Presentations
Microbiomes play essential roles in the health and function of animal and plant hosts and drive nutrient cycling across ecosystems. Integrating novel trait-based approaches with ecological theory can facilitate the prediction of microbial functional traits important for ecosystem functioning and health. In particular, the yield-acquisition-stress (Y-A-S) framework considers dominant microbial life history strategies across gradients of resource availability and stress. However, microbiomes are dynamic, and spatial and temporal shifts in taxonomic and trait composition can affect ecosystem functions. We posit that extending the Y-A-S framework to microbiomes during succession and across biogeographic gradients can lead to generalizable rules for how …
Ecophysiology Of Toxic Bloom-Forming Cyanobacteria And Their Symbionts, Dominique J. Lockwood
Ecophysiology Of Toxic Bloom-Forming Cyanobacteria And Their Symbionts, Dominique J. Lockwood
Masters Theses, 2020-current
Currently, there is a pernicious microbe in the genus Microcystis that is putting the world’s freshwater resources at risk. A member of the phylum Cyanobacteria, otherwise referred to as blue-green algae, Microcystis forms massive algal blooms in lakes and has the potential to produce a toxin, which does not only harm humans, but also pets, livestock, and aquatic life. As recently as 2016, in the city of Toledo, Ohio, nearly 1 million residents went without clean drinking water for an entire weekend due to one of these Microcystis blooms. However, Microcystis does not only bloom in Ohio. In fact, …
Tick Saliva And The Alpha-Gal Syndrome: Finding A Needle In A Haystack, Surendra Raj Sharma, Shahid Karim
Tick Saliva And The Alpha-Gal Syndrome: Finding A Needle In A Haystack, Surendra Raj Sharma, Shahid Karim
Faculty Publications
Ticks and tick-borne diseases are significant public health concerns. Bioactive molecules in tick saliva facilitate prolonged blood-feeding and transmission of tick-borne pathogens to the vertebrate host. Alpha-gal syndrome (AGS), a newly reported food allergy, is believed to be induced by saliva proteins decorated with a sugar molecule, the oligosaccharide galactose-⍺-1,3-galactose (α-gal). This syndrome is characterized by an IgE antibody-directed hypersensitivity against α-gal. The α-gal antigen was discovered in the salivary glands and saliva of various tick species including, the Lone Star tick (Amblyomma americanum). The underlying immune mechanisms linking tick bites with α-gal-specific IgE production are poorly understood and are …
Analysis Of The Slo Bay Microbiome From A Network Perspective, Lien Viet Nguyen
Analysis Of The Slo Bay Microbiome From A Network Perspective, Lien Viet Nguyen
Master's Theses
Microorganisms are key players in the ecosystem functioning. In this thesis, we developed a framework to preprocess raw microbiome data, build a correlation network, and analyze co-occurrence patterns between microbes. We then applied this framework to a marine microbiome dataset. The dataset used in this study comes from a year-long time-series to characterize the microbial communities in our coastal waters off the Cal Poly Pier. In analyzing this dataset, we were able to observe and confirm previously discovered patterns of interactions and generate hypotheses about new patterns. The analysis of co-occurrences between prokaryotic and eukaryotic taxa is relatively novel and …
A Global Metagenomic Map Of Urban Microbiomes And Antimicrobial Resistance, David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista A. Ryon, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar
A Global Metagenomic Map Of Urban Microbiomes And Antimicrobial Resistance, David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista A. Ryon, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar
ISI Best Publications
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and …
Dynamics Of The Soil Microbiome In Ginseng Gardens, Megan E. Lambert
Dynamics Of The Soil Microbiome In Ginseng Gardens, Megan E. Lambert
Electronic Thesis and Dissertation Repository
Ginseng Replant Disease (GRD) is a syndrome in which ginseng cannot be cultivated in soil previously used to grow ginseng. Since GRD can persist for decades, it severely impacts the Ontario ginseng industry. To better understand the origin of GRD, the impact of ginseng cultivation on the soil microbiome was investigated in bulk soil of three newly planted ginseng gardens in Ontario, from seeding through two years of cultivation. While specific trends in species richness, diversity and composition were unclear, PERMANOVA analyses confirmed that they changed over time. Known GRD-related pathogens, including Ilyonectria mors-panacis and Fusarium oxysporum, were detected in …
Rhizosphere Microbiomes In A Historical Maize-Soybean Rotation System Respond To Host Species And Nitrogen Fertilization At The Genus And Subgenus Levels, Michael A. Meier, Martha G. Lopez-Guerrero, Ming Guo, Marty Schmer, Josh Herr, James Schnable, James R. Alfano, Jinliang Yang
Rhizosphere Microbiomes In A Historical Maize-Soybean Rotation System Respond To Host Species And Nitrogen Fertilization At The Genus And Subgenus Levels, Michael A. Meier, Martha G. Lopez-Guerrero, Ming Guo, Marty Schmer, Josh Herr, James Schnable, James R. Alfano, Jinliang Yang
Department of Agronomy and Horticulture: Faculty Publications
Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, …
Microbial-Host Dynamics And The Evolution Of Nearshore Diversity In Hippocampus Abdominalis, Jimiane L. Ashe
Microbial-Host Dynamics And The Evolution Of Nearshore Diversity In Hippocampus Abdominalis, Jimiane L. Ashe
Dissertations, Theses, and Capstone Projects
Local adaptation is a fundamental concept at the core of evolutionary process. Devising means to break down larger concepts and systematically test internal mechanisms are key to understanding the driving forces behind the influence of environmental differences on biological systems. To understand dynamic processes in the natural world, we must strip away layers and confounding variables that may mask the signal we hope to understand. In this case seahorse species, Hippocampus abdominalis, or the pot-bellied seahorse, made an unlikely but ideal study system. The first layer to strip away was neutral genetic variation within the population. A multilocus genetic …
A Research Road Map For Responsible Use Of Agricultural Nitrogen, Michael Udvardi, Frederick E. Below, Michael J. Castellano, Alison J. Eagle, Ken E. Giller, Jagdish Kumar Ladha, Xuejun Liu, Tai Mcclellan Maaz, Barbara Nova-Franco, Nandula Raghuram, G. Philip Robertson, Sonali Roy, Malay Saha, Susanne Schmidt, Mechthild Tegeder, Larry M. York, John W. Peters
A Research Road Map For Responsible Use Of Agricultural Nitrogen, Michael Udvardi, Frederick E. Below, Michael J. Castellano, Alison J. Eagle, Ken E. Giller, Jagdish Kumar Ladha, Xuejun Liu, Tai Mcclellan Maaz, Barbara Nova-Franco, Nandula Raghuram, G. Philip Robertson, Sonali Roy, Malay Saha, Susanne Schmidt, Mechthild Tegeder, Larry M. York, John W. Peters
Agricultural and Environmental Sciences Faculty Research
Nitrogen (N) is an essential but generally limiting nutrient for biological systems. Development of the Haber-Bosch industrial process for ammonia synthesis helped to relieve N limitation of agricultural production, fueling the Green Revolution and reducing hunger. However, the massive use of industrial N fertilizer has doubled the N moving through the global N cycle with dramatic environmental consequences that threaten planetary health. Thus, there is an urgent need to reduce losses of reactive N from agriculture, while ensuring sufficient N inputs for food security. Here we review current knowledge related to N use efficiency (NUE) in agriculture and identify research …
Gut Reactions: Quantitative Predictions Of The Responses Of Human Gut Microbiota To Medical Interventions, Amy Elizabeth Langdon
Gut Reactions: Quantitative Predictions Of The Responses Of Human Gut Microbiota To Medical Interventions, Amy Elizabeth Langdon
Arts & Sciences Electronic Theses and Dissertations
The collection of microbes known as the human microbiome perform vital functions for their host, and when this community becomes unhealthy, its dysbiosis is implicated in a myriad of diseases. The gut microbiota in particular are known to suppress colonization of opportunistic pathogens, regulate the immune system, aid in nutrient breakdown, produce vitamins, and a growing number of other functions. In order to intervene in a dysbiotic microbial ecology, we can try to remove unwanted microbes or try to recolonize the gut with microbes expected to be beneficial. This dissertation provides an overview of the state of medical interventions for …
The Roles Of Capsular Polysaccharides And Diet In The Immune Response To A Bacteroides Thetaiotaomicron Antigen, Samantha Hsieh
The Roles Of Capsular Polysaccharides And Diet In The Immune Response To A Bacteroides Thetaiotaomicron Antigen, Samantha Hsieh
Arts & Sciences Electronic Theses and Dissertations
The environment is well recognized to modulate immune responses within the intestinal mucosa in a general fashion. However, the connection between the effects of the environment on the immune response directed towards specific intestinal microbes is unclear. Progress in this area has been hampered by the lack of a model system in which the immune responses to a specific antigen in a gut symbiont can be examined. To this end, we developed a novel CD4+ T cell model, termed BθOM, that is specific for a dominant antigen in the gut symbiont Bacteroides thetaiotaomicron (B. theta). In this work, we use …
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 …
Effects Of Bacterial Metabolites In Conditioned Media On Colon Cancer Proliferation, Hunter Panier
Effects Of Bacterial Metabolites In Conditioned Media On Colon Cancer Proliferation, Hunter Panier
Master's Theses
Cancer is the second leading cause of death in the United States with colorectal cancer (CRC) being the third most common type. Available treatments include a combination of surgery and chemotherapy but have debilitating side effects. These also have limited effectiveness in some cases, creating the need for additional treatment options, or supplementary treatments to increase their effectiveness. This is leading scientists to consider the microbiome to fix this shortcoming. Current research is focusing on the microbiome and its interactions with certain diseases, which could lead to pro- or prebiotic therapies. This work aims to establish specific bacterial species can …
How Historic Shipwrecks Influence Dispersal Of Deep-Sea Microbiomes, Rachel Moseley
How Historic Shipwrecks Influence Dispersal Of Deep-Sea Microbiomes, Rachel Moseley
Master's Theses
This thesis investigates how historic shipwrecks potentially shape dispersal of deep-sea microbiomes. Processes impacting dispersal of microbiomes around artificial structures in the ocean and how they connect to other deep-sea habitats is unknown. Dispersal processes are explained for some macroorganisms by theories in ecology, specifically the Theory of Island Biogeography and the Wooden Stepping Stone hypothesis. These have not been investigated for microorganisms, and thus this work will probe if they are applicable to microbial biogeography in this habitat. Experiments were conducted to establish new “island-like” features in near proximity (25-125 m) to wooden-hulled historic shipwrecks in the northern Gulf …
Unraveling Host-Gut Microbiota Dialogue And Its Impact On Response To Immune Checkpoint Blockade, Alexandria Cogdill
Unraveling Host-Gut Microbiota Dialogue And Its Impact On Response To Immune Checkpoint Blockade, Alexandria Cogdill
Dissertations & Theses (Open Access)
Cancer is a disease with only one degree of separation, affecting one in two men and one in three women in their lifetimes; accounting for 1 of every 6 deaths. While cancer mortality rates continue to improve, incidence rates are expected to rise and shift through 2050 due to epidemiological and demographic transitions worldwide. As such, it is imperative to continue to investigate and improve our understanding of both disease etiology and hallmarks of response to treatment. Currently, conventional therapies include, but are not limited to, surgery, chemotherapy, and radiotherapy. However, within the past decade, major advances have been made …
Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke
Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke
Computer Science and Computer Engineering Undergraduate Honors Theses
Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …