Health Care and the Middle Class: More Costs and Less Coverage

Examines the availability, affordability, and stability of health insurance coverage for middle-income families; trends contributing to their growing medical cost burden and percentage among the newly uninsured; and implications

MS Environmental Biology Capstone Project

Chapter 1: Artificial light at night disrupts the biology of fishes. Chapter 2: Grant proposal to determine how artificial light at night affects Pumpkinseed fish. Chapter 3: Management of pinyon-juniper woodland impacts the occupancy of Pinyon Jays. Chapter 4: Stakeholder analysis of horseshoe crab fishing and its impacts on the Red Knot and biomedical industry

UPΦ phages, a new group of filamentous phages found in several members of Enterobacteriales

Filamentous phages establish chronic infections in their bacterial hosts, and new phages are secreted by infected bacteria for multiple generations, typically without causing host death. Often, these viruses integrate in their host’s genome by co-opting the host’s XerCD recombinase system. In several cases, these viruses also encode genes that increase bacterial virulence in plants and animals. Here, we describe a new filamentous phage, UPϕ901, which we originally found integrated in a clinical isolate of Escherichia coli from urine. UPϕ901 and closely related phages can be found in published genomes of over 200 other bacteria, including strains of Citrobacter koseri, Salmonella enterica, Yersinia enterocolitica, and Klebsiella pneumoniae. Its closest relatives are consistently found in urine or in the blood and feces of patients with urinary tract infections. More distant relatives can be found in isolates from other environments, including sewage, water, soil, and contaminated food. Each of these phages, which we collectively call ‘UPϕ viruses’, also harbors two or more novel genes of unknown function

The State of Civics Education

The policy solution that has garnered the most momentum to improve civics in recent years is a standard that requires high school students to pass the U.S. citizenship exam before graduation. According to this analysis, 17 states have taken this path. Yet, critics of a mandatory civics exam argue that the citizenship test does nothing to measure comprehension of the material and creates an additional barrier to high school graduation. Other states have adopted civics as a requirement for high school graduation, provided teachers with detailed civics curricula, offered community service as a graduation requirement, and increased the availability of Advance Placement (AP) U. S. government classes. When civics education is taught effectively, it can equip students with the knowledge, skills, and disposition necessary to become informed and engaged citizens. Educators must also remember that civics is not synonymous with history. While increasing history courses and service requirements are potential steps to augment students' background knowledge and skill sets, civics is a narrow and instrumental instruction that provides students with the agency to apply these skills. This analysis finds a wide variation in state requirements and levels of youth engagement. While this research highlights that no state currently provides sufficient and comprehensive civic education, there is reason to be optimistic that high-quality civics education can impact civic behavior

Rephine.r: A pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies

Background. A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools. Methods. We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees. Results. We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny. The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single script for automated analysis and with utility functions to assist in building single-copy core genomes and predicting the sources of fragmented genes

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution

Bacteriophages are the most abundant and diverse biological entities on the planet, and new phage genomes are being discovered at a rapid pace. As more phage genomes are published, new methods are needed for placing these genomes in an ecological and evolutionary context. Phages are difficult to study by phylogenetic methods, because they exchange genes regularly, and no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide a high-resolution view of phage genetic diversity and offer a novel perspective on virus ecology. We focus our analyses on virus host range and show how network topology corresponds to host relatedness, how to find groups of genes with the strongest host-specific signatures, and how this perspective can complement phage host prediction tools. We discuss extensions of gene network analysis to predicting the emergence of phages on new hosts, as well as applications to features of phage biology beyond host range

The Hall of Mirrors Perceptions and Misperceptions in the Congressional Foreign Policy Process

Explores several factors related to an inconsistency in the voting record by the U.S. Congress on foreign policy issues, compared with the position taken by the public, administration officials, and leaders in business, labor, media, and education

Cooking and co-ingested polyphenols reduce in vitro methylmercury bioaccessibility from fish and may alter exposure in humans

Fish consumption is a major pathway for mercury exposure in humans. Current guidelines and risk assessments assume that 100% of methylmercury (MeHg) in fish is absorbed by the human body after ingestion. However, a growing body of literature suggests that this absorption rate may be overestimated. We used an in vitro digestion method to measure MeHg bioaccessibility in commercially-purchased fish, and investigated the effects of dietary practices on MeHg bioaccessibility. Cooking had the greatest effect, decreasing bioaccessibility on average to 12.5 ± 5.6%. Polyphenol-rich beverages also significantly reduced bioaccessibility to 22.7 ± 3.8% and 28.6 ± 13.9%, for green and black tea respectively. We confirmed the suspected role of polyphenols in tea as being a driver of MeHg's reduced bioaccessibility, and found that epicatechin, epigallocatechin gallate, rutin and cafeic acid could individually decrease MeHg bioaccessibility by up to 55%. When both cooking and polyphenol-rich beverage treatments were combined, only 1% of MeHg remained bioaccessible. These results call for in vivo validation, and suggest that dietary practices should be considered when setting consumer guidelines for MeHg. More realistic risk assessments could promote consumption of fish as a source of fatty acids, which can play a protective role against cardiovascular disease

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality

Lactobacilli are dominant members of the “healthy” female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction between genomes of the two species. We find eight additional strains of the species L. mulieris among these genomes. Furthermore, one strain, currently classified as L. mulieris UMB7784, is distinct from both L. jensenii and L. mulieris strains. As part of our comparative genomic study, we also investigated the genetic content that distinguishes these two species. Unique to the L. jensenii genomes are several genes related to catabolism of disaccharides. In contrast, L. mulieris genomes encode several cell surface and secreted proteins that are not found within the L. jensenii genomes. These L. jensenii-specific and L. mulieris-specific loci provide insight into phenotypic differences of these two species