Publications by authors named "S Donovan"

384 Publications

Emerging Science, Personal Protective Equipment Guidance, and Resource Scarcity: Inaction and Inequity for Workers in Essential Industries.

Health Secur 2021 Jun 9. Epub 2021 Jun 9.

Abigail E. Lowe, MA, is Director, Ethics and Public Health Preparedness; Jocelyn J. Herstein, PhD, MPH, is a Research Assistant Professor; David M. Brett-Major, MD, MPH, is a Professor; and Rachel E. Lookadoo, JD, is Director, Legal and Public Health Preparedness, and Instructor; all in the College of Public Health, University of Nebraska Medical Center, Omaha, NE. Kelly K. Dineen, JD, PhD, is Director, Health Law Program; an Associate Professor of Law; and a Professor of Medical Humanities; all at Creighton University School of Law, Omaha, NE. Matthew K. Wynia, MD, MPH, is Director, Center for Bioethics and Humanities, and a Professor of Medicine and Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO. Joshua L. Santarpia, PhD, MS, is an Associate Professor, College of Medicine; Research Director, Chemical and Biological Programs, National Strategic Research Institute; and Co-Director of Biological Defense and Health Security-Sub Plan, Graduate Studies; all at the University of Nebraska Medical Center, Omaha, NE. Lisa M. Lee, PhD, MA, MS, is Associate Vice President, Research and Innovation; Director, Scholarly Integrity and Research Compliance, Office of the Vice President for Research and Innovation; and a Research Professor, Department of Population Health Sciences; all at Virginia Tech, Blacksburg, VA. Alva O. Ferdinand, DrPH, JD, is an Associate Professor and Director of Southwest Rural Health Research Center, Texas A&M University School of Public Health, College Station, TX. Sara K. Donovan, MPH, is a Doctoral Student, Graduate Studies, and Graduate Research Assistant, Global Center for Health Security; both at the University of Nebraska Medical Center, Omaha, NE. Teck Chuan Voo, PhD, is an Assistant Professor, Centre for Biomedical Ethics, NUS Yong Loo Lin School of Medicine, Singapore. Seema Mohapatra, JD, MPH, is a Dean's Fellow and Associate Professor, Robert H. McKinney School of Law, Indiana University, Indianapolis, IN.

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http://dx.doi.org/10.1089/hs.2021.0040DOI Listing
June 2021

A Systematic Review of Dietary Influences on Fecal Microbiota Composition and Function among Healthy Humans 1-20 Years of Age.

Adv Nutr 2021 May 5. Epub 2021 May 5.

Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.

Diet is a key modulator of fecal microbiota composition and function. However, the influence of diet on the microbiota from toddlerhood to adolescence and young adulthood is less well studied than for infancy and adulthood. We aimed to complete a qualitative systematic review of the impacts of diet on the fecal microbiota of healthy humans 1-20 y of age. English-language articles, published after 2008, indexed in the PubMed/MEDLINE, Cochrane, Web of Science, and Scopus databases were searched using keywords and Medical Subject Headings terms. Quality assessment of included studies was conducted using the Quality Criteria Checklist derived from the Nutrition Evidence Library of the Academy of Nutrition and Dietetics. A total of 973 articles were identified through database searching and 3 additional articles were included via cross-reference. Subsequent to de-duplication, 723 articles were screened by title and abstract, of which 709 were excluded based on inclusion criteria established a priori. The remaining 14 studies were independently screened by 2 reviewers for final inclusion. Included studies were published between 2010 and 2019 and included 8 comparative cross-sectional studies, 4 cross-sectional studies, 1 randomized crossover study, and 1 substudy of a randomized 2-period crossover trial. Associations of a diet rich in indigestible plant polysaccharides with Prevotella, or with an enterotype dominated by this genus, often comprised of the species Prevotella copri, were observed. In addition, associations of a high-fat and -sugar diet with Bacteroides, or with an enterotype dominated by this genus, were observed predominantly in comparative cross-sectional and cross-sectional studies spanning the ages of 1-15 y. This review identified a gap in the literature for ages 16-20 y. In addition, randomized controlled trials for dietary intervention are needed to move from association-based observations to causal relations between diet and microbiota composition and function. This systematic review was registered at www.crd.york.ac.uk/prospero as CRD42020129824.
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http://dx.doi.org/10.1093/advances/nmab047DOI Listing
May 2021

Exfoliated Epithelial Cell Transcriptome Reflects Both Small and Large Intestinal Cell Signatures in Piglets.

Am J Physiol Gastrointest Liver Physiol 2021 May 5. Epub 2021 May 5.

Nutrition and Food Science, grid.264756.4Texas A&M University.

Assessing intestinal development and host-microbe interactions in healthy human infants requires non-invasive approaches. We have shown that the transcriptome of exfoliated epithelial cells in feces can differentiate breast and formula-fed infants and term and preterm infants. However, it is not fully understood which regions of the intestine that the exfoliated cells represent. Herein, the transcriptional profiles of exfoliated cells with that of the ileal and colonic mucosa were compared. We hypothesized that exfoliated cells in the distal colon would reflect mucosal signatures of more proximal regions of the gut. Two-d-old piglets (n=8) were fed formulas for 20 d. Luminal contents and mucosa were collected from ileum (IL), ascending (AC) and descending (DC) colon, mRNA was extracted and sequenced. On average, ~ 13,000 genes were mapped in mucosal tissues and ~10,000 in luminal contents. The intersection of detected genes between 3 mucosa regions and DC exfoliome indicated an approximately 99% overlap. On average, 49% of the genes in IL, AC and DC mucosa were present in the AC and DC exfoliome. Genes expressed predominantly in specific anatomic sites (stomach, pancreas, small intestine, colon) were detectable in exfoliated cells. Additionally, gene markers for all intestinal epithelial cell types were expressed in the exfoliome representing a diverse array of cell types arising from both the small and large intestine. Genes were mapped to nutrient absorption and transport and immune function. Thus, the exfoliome represents a robust reservoir of information in which to assess intestinal development and responses to dietary interventions.
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http://dx.doi.org/10.1152/ajpgi.00017.2021DOI Listing
May 2021

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways.

Genome Biol 2021 May 3;22(1):132. Epub 2021 May 3.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.

Background: Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing splicing pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses.

Results: RNA immunoprecipitation in tandem (RIPiT) of exon junction complex components allows for purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and, therefore, translation-dependent mRNA decay. Here we compare exon junction complex RIPiT-Seq to whole cell RNA-Seq data from HEK293 cells. Consistent with expectation, the flux through known AS-NMD pathways is substantially higher than that captured by RNA-Seq. Our RIPiT-Seq also definitively demonstrates that the splicing machinery itself has no ability to detect reading frame. We identify thousands of previously unannotated splicing events; while many can be attributed to splicing noise, others are evolutionarily conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis.

Conclusions: Deep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the nonsense-mediated decay-linked alternative splicing pathway predominates. Exon junction complex RIPiT-Seq also revealed numerous conserved but previously unannotated AS-NMD events.
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http://dx.doi.org/10.1186/s13059-021-02309-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8091538PMC
May 2021

A Mediation Analysis to Identify Links between Gut Bacteria and Memory in Context of Human Milk Oligosaccharides.

Microorganisms 2021 Apr 15;9(4). Epub 2021 Apr 15.

Traverse Science, Inc., Champaign, IL 61820, USA.

Elucidating relationships between the gut and brain is of intense research focus. Multiple studies have demonstrated that modulation of the intestinal environment via prebiotics or probiotics can induce cognitively beneficial effects, such as improved memory or reduced anxiety. However, the mechanisms by which either act remain largely unknown. We previously demonstrated that different types of oligosaccharides affected short- and long-term memory in distinct ways. Given that the oligosaccharide content of human milk is highly variable, and that formula-fed infants typically do not consume similar amounts or types of oligosaccharides, their potential effects on brain development warrant investigation. Herein, a mediation analysis was performed on existing datasets, including relative abundance of bacterial genera, gene expression, brain volume, and cognition in young pigs. Analyses revealed that numerous bacterial genera in both the colon and feces were related to short- and/or long-term memory. Relationships between genera and memory appeared to differ between diets. Mediating variables frequently included GABAergic and glutamatergic hippocampal gene expression. Other mediating variables included genes related to myelination, transcription factors, brain volume, and exploratory behavior. Overall, this analysis identified multiple pathways between the gut and brain, with a focus on genes related to excitatory/inhibitory neurotransmission.
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http://dx.doi.org/10.3390/microorganisms9040846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8071191PMC
April 2021