11 results on '"Joseph D. Madison"'
Search Results
2. Stochasticity and Randomness in Community Assembly: Real or As-If?
- Author
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Joseph D. Madison
- Subjects
Microbiology ,QR1-502 - Published
- 2021
- Full Text
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Catalog
3. Porphyromonas somerae Invasion of Endometrial Cancer Cells
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Taylor A. Crooks, Joseph D. Madison, Dana M. Walsh, William G. Herbert, Patricio R. Jeraldo, Nicholas Chia, William A. Cliby, Scott H. Kaufmann, and Marina R. S. Walther-Antonio
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Porphyromonas somerae ,endometrial cancer ,estradiol ,intracellular invasion ,succinate dehydrogenase ,fumarate reductase ,Microbiology ,QR1-502 - Abstract
Recent evidence suggests an association between endometrial cancer and the understudied bacterial species Porphyromonas somerae. This association was demonstrated in previous work that indicated a significantly enriched abundance of P. somerae in the uterine microbiome of endometrial cancer patients. Given the known associations of the Porphyromonas genus and oral cancer, we hypothesized that P. somerae may play a similar pathogenic role in endometrial cancer via intracellular activity. Before testing our hypothesis, we first characterized P. somerae biology, as current background data is limited. These novel characterizations include growth curves in liquid medium and susceptibility tests to antibiotics. We tested our hypothesis by examining growth changes in response to 17β-estradiol, a known risk factor for endometrial cancer, followed by metabolomic profiling in the presence and absence of 17β-estradiol. We found that P. somerae exhibits increased growth in the presence of 17β-estradiol of various concentrations. However, we did not find significant changes in metabolite levels in response to 17β-estradiol. To study direct host-microbe interactions, we used in vitro invasion assays under hypoxic conditions and found evidence for intracellular invasion of P. somerae in endometrial adenocarcinoma cells. We also examined these interactions in the presence of 17β-estradiol but did not observe changes in invasion frequency. Invasion was shown using three lines of evidence including visualization via differential staining and brightfield microscopy, increased frequency of bacterial recovery after co-culturing, and in silico methods to detail relevant genomic and transcriptomic components. These results underscore potential intracellular phenotypes of P. somerae within the uterine microbiome. Furthermore, these results raise new questions pertaining to the role of P. somerae in the progression of endometrial cancer. more...
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- 2021
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4. The USD Science Gateway: A Bridge Between Research and Advanced Computing.
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Adison A. Kleinsasser, Sudhakar Pamidighantam, Douglas M. Jennewein, Joseph D. Madison, Marcus Christie, Eroma Abeysinghe, Suresh Marru, and Marlon E. Pierce
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- 2019
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5. Science Gateway Implementation at the University of South Dakota: Applications in Research and Education.
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Joseph D. Madison, Eroma Abeysinghe, Sudhakar Pamidighantam, Suresh Marru, Marcus Christie, Douglas M. Jennewein, and Marlon E. Pierce
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- 2018
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6. Microbial communities as interactors
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Joseph D. Madison
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History ,History and Philosophy of Science ,General Social Sciences - Published
- 2022
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7. Bacterial Microbiota Response inGraptemys pseudogeographicato Captivity and Roundup®Exposure
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Joseph D. Madison, Drew R. Davis, Shaylyn Austin, and Jacob L. Kerby
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0301 basic medicine ,Graptemys pseudogeographica ,biology ,030106 microbiology ,Zoology ,Captivity ,Context (language use) ,Aquatic Science ,biology.organism_classification ,law.invention ,03 medical and health sciences ,Microbial population biology ,Habitat ,law ,Animal Science and Zoology ,Microbiome ,Cloaca ,Turtle (robot) ,Ecology, Evolution, Behavior and Systematics - Abstract
Understanding how environmental factors influence various aspects of freshwater turtle health remains an important yet understudied topic within the context of individual–environment interactions. This is particularly true of host-associated bacterial microbiota, which are being increasingly recognized as a significant and understudied topic in the context of individual turtle health. While this area of work has expanded in certain areas, research efforts remain limited with regard to host–microbiota interactions in the context of habitat contaminants. Specifically, the commonly used herbicide, glyphosate, is of interest due to its massive worldwide use and known effects on various organisms. Effects of captivity on host-associated microbial community structure also remain largely unknown in various non-model organisms. To address these unknown effects of Roundup® and captivity on host-associated microbiomes, we examined the effects of low-level Roundup® exposure and captivity on the cloacal microbiota of the False Map Turtle, Graptemys pseudogeographica. We determined the effect of glyphosate by taking cloacal swabs pre- (0 h) and post-exposure (72 h) and examined microbial community beta- and alpha-diversity through 16S rRNA gene high-throughput sequencing. The results of this study indicate that low-level, short-term glyphosate exposure does not significantly alter the microbiota structure of G. pseudogeographica. However, there was a significant decrease in microbial community beta-diversity over time, confirming a trend that has been observed to a limited extent in other non-model organisms when put in laboratory conditions. These results are useful in understanding the baseline cloaca microbial community structure of G. pseudogeographica, as well as the implications and limitations of laboratory-based microbiota studies. Furthermore, this work suggests that low-level and short-term glyphosate exposure does not have a significant effect on the cloacal microbial community structure in wild-caught G. pseudogeographica. more...
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- 2018
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8. Design‐ and model‐based recommendations for detecting and quantifying an amphibian pathogen in environmental samples
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Kathryn P. Huyvaert, Brittany A. Mosher, Larissa L. Bailey, Tara Chestnut, Joseph D. Madison, and Jacob L. Kerby
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0106 biological sciences ,0301 basic medicine ,Amphibian ,Pathogen detection ,Occupancy ,Batrachochytrium dendrobatidis ,Zoology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Chytridiomycosis ,Abundance (ecology) ,biology.animal ,Environmental DNA ,Pathogen ,Ecology, Evolution, Behavior and Systematics ,Original Research ,Nature and Landscape Conservation ,filtration ,Ecology ,biology ,host‐pathogen dynamics ,biology.organism_classification ,qPCR ,monitoring ,030104 developmental biology ,detection probability ,eDNA ,multiscale occupancy - Abstract
Accurate pathogen detection is essential for developing management strategies to address emerging infectious diseases, an increasingly prominent threat to wildlife. Sampling for free‐living pathogens outside of their hosts has benefits for inference and study efficiency, but is still uncommon. We used a laboratory experiment to evaluate the influences of pathogen concentration, water type, and qPCR inhibitors on the detection and quantification of Batrachochytrium dendrobatidis (Bd) using water filtration. We compared results pre‐ and post‐inhibitor removal, and assessed inferential differences when single versus multiple samples were collected across space or time. We found that qPCR inhibition influenced both Bd detection and quantification in natural water samples, resulting in biased inferences about Bd occurrence and abundance. Biases in occurrence could be mitigated by collecting multiple samples in space or time, but biases in Bd quantification were persistent. Differences in Bd concentration resulted in variation in detection probability, indicating that occupancy modeling could be used to explore factors influencing heterogeneity in Bd abundance among samples, sites, or over time. Our work will influence the design of studies involving amphibian disease dynamics and studies utilizing environmental DNA (eDNA) to understand species distributions. more...
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- 2017
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9. Serratia marcescens shapes cutaneous bacterial communities and influences survival of an amphibian host
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Jacob L. Kerby, Scot P. Ouellette, Emme L Schmidt, and Joseph D. Madison
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0106 biological sciences ,Amphibian ,010603 evolutionary biology ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,Microbiology ,Prodigiosin ,03 medical and health sciences ,chemistry.chemical_compound ,Microbial ecology ,biology.animal ,Microbiome ,Chytridiomycosis ,030304 developmental biology ,General Environmental Science ,0303 health sciences ,Ecology ,General Immunology and Microbiology ,biology ,Host (biology) ,General Medicine ,biology.organism_classification ,Genetically modified organism ,chemistry ,Serratia marcescens ,General Agricultural and Biological Sciences - Abstract
Ongoing investigations into the interactions between microbial communities and their associated hosts are changing how emerging diseases are perceived and ameliorated. Of the numerous host–microbiome–disease systems of study, the emergence of chytridiomycosis (caused by Batrachochytrium dendrobatidis , hereafter Bd ) has been implicated in ongoing declines and extinction events of amphibians worldwide. Interestingly, there has been differential survival among amphibians in resisting Bd infection and subsequent disease. One factor thought to contribute to this resistance is the host-associated cutaneous microbiota. This has raised the possibility of using genetically modified probiotics to restructure the host-associated microbiota for desired anti-fungal outcomes. Here, we use a previously described strain of Serratia marcescens ( Sm ) for the manipulation of amphibian cutaneous microbiota. Sm was genetically altered to have a dysfunctional pathway for the production of the extracellular metabolite prodigiosin. This genetically altered strain (Δ pig ) and the functional prodigiosin producing strain (wild-type, WT) were compared for their microbial community and anti- Bd effects both in vitro and in vivo . In vitro , Bd growth was significantly repressed in the presence of prodigiosin. In vivo , the inoculation of both Sm strains was shown to significantly influence amphibian microbiota diversity with the Δ pig-Sm treatment showing increasing alpha diversity, and the WT- Sm having no temporal effect on diversity. Differences were also seen in host mortality with Δ pig-Sm treatments exhibiting significantly decreased survival probability when compared with WT- Sm in the presence of Bd . These results are an important proof-of-concept for linking the use of genetically modified probiotic bacteria to host microbial community structure and disease outcomes, which in the future may provide a way to ameliorate disease and address critical frontiers in disease and microbial ecology. more...
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- 2019
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10. Characterization of Batrachochytrium dendrobatidis Inhibiting Bacteria from Amphibian Populations in Costa Rica
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Elizabeth A. Berg, Jacob L. Kerby, Steven M. Whitfield, Juan G. Abarca, Joseph D. Madison, Adrian Pinto, and Oxana Gorbatenko
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0301 basic medicine ,Microbiology (medical) ,Amphibian ,Population ,RNA-sequencing ,microbiome ,Zoology ,Fungus ,Microbiology ,03 medical and health sciences ,biology.animal ,Microbiome ,education ,Batrachochytrium dendrobatidis ,Serratia marcescens ,education.field_of_study ,Extinction ,biology ,Resistance (ecology) ,biology.organism_classification ,3. Good health ,030104 developmental biology ,amphibian ,Bacteria - Abstract
Global amphibian declines and extinction events are occurring at an unprecedented rate. While several factors are responsible for declines and extinction, the fungal pathogen Batrachochytrium dendrobatidis (Bd) has been cited as a major constituent in these events. While the effects of this chytrid fungus have been shown to cause broad scale population declines and extinctions, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous bacterial microbiome. Here, we present the first study characterizing anti-Bd bacterial isolates from amphibian populations in Costa Rica, including the characterization of two strains of Serratia marcescens presenting strong anti-Bd activity. Transcriptome sequencing was utilized for delineation of shifts in gene expression of the two previously uncharacterized strains of S. marcescens grown in three different treatments comprising Bd, heat-killed Bd, and a no Bd control. These results revealed up- and down-regulation of key genes associated with different metabolic and regulatory pathways. This information will be valuable in continued efforts to develop a bacterial-based approach for amphibian protection as well as providing direction for continued mechanistic inquiries of the bacterial anti-Bd response. Fish and Wildlife Service/[46-6003541]/USFWS/Estados Unidos Universidad de Costa Rica/[801-B2-029]/UCR/Costa Rica General Medicine Sciences of the National Institutes of Health/[P20GM103443]7NIGMS/Estados Unidos UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC) UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM) UCR::Vicerrectoría de Docencia::Salud::Facultad de Medicina::Escuela de Medicina more...
- Published
- 2017
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11. Characterization of
- Author
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Joseph D, Madison, Elizabeth A, Berg, Juan G, Abarca, Steven M, Whitfield, Oxana, Gorbatenko, Adrian, Pinto, and Jacob L, Kerby
- Subjects
RNA-sequencing ,microbiome ,amphibian ,Microbiology ,Batrachochytrium dendrobatidis ,Serratia marcescens ,Original Research - Abstract
Global amphibian declines and extinction events are occurring at an unprecedented rate. While several factors are responsible for declines and extinction, the fungal pathogen Batrachochytrium dendrobatidis (Bd) has been cited as a major constituent in these events. While the effects of this chytrid fungus have been shown to cause broad scale population declines and extinctions, certain individuals and relict populations have shown resistance. This resistance has been attributed in part to the cutaneous bacterial microbiome. Here, we present the first study characterizing anti-Bd bacterial isolates from amphibian populations in Costa Rica, including the characterization of two strains of Serratia marcescens presenting strong anti-Bd activity. Transcriptome sequencing was utilized for delineation of shifts in gene expression of the two previously uncharacterized strains of S. marcescens grown in three different treatments comprising Bd, heat-killed Bd, and a no Bd control. These results revealed up- and down-regulation of key genes associated with different metabolic and regulatory pathways. This information will be valuable in continued efforts to develop a bacterial-based approach for amphibian protection as well as providing direction for continued mechanistic inquiries of the bacterial anti-Bd response. more...
- Published
- 2016
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