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Public stigma towards people with mental illness is often comprised of incorrect beliefs and stereotypes about dangerousness and social and interpersonal deficits. Past research has examined the impact that one’s personality and upbringing have on the willingness to endorse stigmatizing beliefs. While results have been mixed, low prosocial personality traits (Yuan et al., 2018) and high parental control/overprotectiveness (Zhao et al., 2015) have been shown to predict higher levels of mental illness stigma. Currently, no study has examined potential interaction effects between these factors; it is possible that higher levels of prosocial personality traits may lessen the impact controlling parenting has on mental illness stigma through the facilitation of contact experiences with stigmatized individuals, which commonly contributes to reduced endorsement of stigma (Yuan et al., 2018). It was predicted that controlling parenting would be positively associated with the endorsement of beliefs that mentally ill individuals are dangerous and possess poor social skills, and that this association would be lessened by high prosocial personality traits such as Agreeableness, Extraversion, and Openness. An overall sample of 268 participants between the ages of 18 and 24 were recruited from two separate online platforms and reported on measures of recalled parental overprotectiveness, personality traits, and stigmatizing beliefs. The present findings indicate that none of the interaction effects between parenting and personality were significant. Correlational analyses indicate that high Agreeableness and Openness predict lower perceived dangerousness and low social skills, while Extraversion shows a negative association with perceived poor social skills. Parental overprotectiveness displayed no significant correlations with any stigma measures, while regression models indicated that high parental overcontrol contributes to perceived poor social and interpersonal skills for men

A common practice in many transport models is to allocate all costs to the car driver meaning that car passengers are essentially free riders. This specification provides an easy way of integrating drivers and passengers and fits well with the general understanding that car drivers rarely trade passenger seats for money. However, in this paper, we question this premise and argue that cost sharing can, and most likely will, take place in a variety of forms different from simple out-off-pocket money exchange. We also stress that from a modelling perspective, this issue is far from irrelevant as it influences not only demand elasticities but also the modelling of car occupancy rates which is one of the key variables when considering congestion, climate impacts, and network utilisation. In the paper we discuss the mechanisms by which costs are shared, consider how this can be operationalised in transport models, and finally, consider the consequences of cost sharing from a transport policy perspective. Based on empirical evidence from Denmark, we find that for trip purposes with high occupancy rates, cost elasticities and occupancy rates tend to be biased if cost sharing is not properly accounted for.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Amaral, V., Lam, P., Marchal, O., Roca-Martí, M., Fox, J., & Nelson, N. Particle cycling rates at Station P as estimated from the inversion of POC concentration data. Elementa: Science of the Anthropocene, 10(1), (2022): 00018, https://doi.org/10.1525/elementa.2021.00018., Particle cycling rates in marine systems are difficult to measure directly, but of great interest in understanding how carbon and other elements are distributed throughout the ocean. Here, rates of particle production, aggregation, disaggregation, sinking, remineralization, and transport mediated by zooplankton diel vertical migration were estimated from size-fractionated measurements of particulate organic carbon (POC) concentration collected during the NASA EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) cruise at Station P in summer 2018. POC data were combined with a particle cycling model using an inverse method. Our estimates of the total POC settling flux throughout the water column are consistent with those derived from thorium-234 disequilibrium and sediment traps. A budget for POC in two size fractions, small (1–51 µm) and large (> 51 µm), was produced for both the euphotic zone (0–100 m) and the upper mesopelagic zone (100–500 m). We estimated that POC export at the base of the euphotic zone was 2.2 ± 0.8 mmol m−2 d−1, and that both small and large particles contributed considerably to the total export flux along the water column. The model results indicated that throughout the upper 500 m, remineralization leads to a larger loss of small POC than does aggregation, whereas disaggregation results in a larger loss of large POC than does remineralization. Of the processes explicitly represented in the model, zooplankton diel vertical migration is a larger source of large POC to the upper mesopelagic zone than the convergence of large POC due to particle sinking. Positive model residuals reveal an even larger unidentified source of large POC in the upper mesopelagic zone. Overall, our posterior estimates of particle cycling rate constants do not deviate much from values reported in the literature, i.e., size-fractionated POC concentration data collected at Station P are largely consistent with prior estimates given their uncertainties. Our budget, This study was supported by the National Aeronautics and Space Administration (NASA) program award 80NSSC17K0555, NSF-OCE 1829614 to PJL, and NSF-OCE-1829790 to OM. VJA was supported by the NSF Graduate Research Fellowship Program and the UC Eugene Cota-Robles Fellowship. MRM was supported by the Ocean Frontier Institute International Postdoctoral Fellowship Program and the Woods Hole Oceanographic Institution’s Ocean Twilight Zone study.

Causal reasoning and game-theoretic reasoning are fundamental topics in artificial intelligence, among many other disciplines: this paper is concerned with their intersection. Despite their importance, a formal framework that supports both these forms of reasoning has, until now, been lacking. We offer a solution in the form of (structural) causal games, which can be seen as extending Pearl's causal hierarchy to the game-theoretic domain, or as extending Koller and Milch's multi-agent influence diagrams to the causal domain. We then consider three key questions: i) How can the (causal) dependencies in games - either between variables, or between strategies - be modelled in a uniform, principled manner? ii) How may causal queries be computed in causal games, and what assumptions does this require? iii) How do causal games compare to existing formalisms? To address question i), we introduce mechanised games, which encode dependencies between agents' decision rules and the distributions governing the game. In response to question ii), we present definitions of predictions, interventions, and counterfactuals, and discuss the assumptions required for each. Regarding question iii), we describe correspondences between causal games and other formalisms, and explain how causal games can be used to answer queries that other causal or game-theoretic models do not support. Finally, we highlight possible applications of causal games, aided by an extensive open-source Python library., Comment: Published in Artificial Intelligence (2023)

Megakaryocytes (MKs) are precursors to platelets, the second most abundant cells in the peripheral circulation. However, while platelets are known to participate in immune responses and play significant functions during infections, the role of MKs within the immune system remains largely unexplored. Histological studies of sepsis patients identified increased nucleated CD61+ cells (MKs) in the lungs, and CD61+ staining (likely platelets within microthrombi) in the kidneys, which correlated with the development of organ dysfunction. Detailed imaging cytometry of peripheral blood from patients with sepsis found significantly higher MK counts, which we predict would likely be misclassified by automated hematology analyzers as leukocytes. Utilizing in vitro techniques, we show that both stem cell derived MKs (SC MKs) and cells from the human megakaryoblastic leukemia cell line, Meg-01, undergo chemotaxis, interact with bacteria, and are capable of releasing chromatin webs in response to various pathogenic stimuli. Together, our observations suggest that MK cells display some basic innate immune cell behaviors and may actively respond and play functional roles in the pathophysiology of sepsis.

Helicobacter spp., including the well-known human gastric pathogen H. pylori, can cause gastric diseases in humans and other mammals. They are Gram-negative bacteria that colonize the gastric epithelium and use their multiple flagella to move across the protective gastric mucus layer. The flagella of different Helicobacter spp. vary in their location and number. This review focuses on the swimming characteristics of different species with different flagellar architectures and cell shapes. All Helicobacter spp. use a run-reverse-reorient mechanism to swim in aqueous solutions, as well as in gastric mucin. Comparisons of different strains and mutants of H. pylori varying in cell shape and the number of flagella show that their swimming speed increases with an increasing number of flagella and is somewhat enhanced with a helical cell body shape. The swimming mechanism of H. suis, which has bipolar flagella, is more complex than that of unipolar H. pylori. H. suis exhibits multiple modes of flagellar orientation while swimming. The pH-dependent viscosity and gelation of gastric mucin significantly impact the motility of Helicobacter spp. In the absence of urea, these bacteria do not swim in mucin gel at pH < 4, even though their flagellar bundle rotates.

Given rapid progress toward advanced AI and risks from frontier AI systems (advanced AI systems pushing the boundaries of the AI capabilities frontier), the creation and implementation of AI governance and regulatory schemes deserves prioritization and substantial investment. However, the status quo is untenable and, frankly, dangerous. A regulatory gap has permitted AI labs to conduct research, development, and deployment activities with minimal oversight. In response, frontier AI system evaluations have been proposed as a way of assessing risks from the development and deployment of frontier AI systems. Yet, the budding AI risk evaluation ecosystem faces significant coordination challenges, such as a limited diversity of evaluators, suboptimal allocation of effort, and perverse incentives. This paper proposes a solution in the form of an international consortium for AI risk evaluations, comprising both AI developers and third-party AI risk evaluators. Such a consortium could play a critical role in international efforts to mitigate societal-scale risks from advanced AI, including in managing responsible scaling policies and coordinated evaluation-based risk response. In this paper, we discuss the current evaluation ecosystem and its shortcomings, propose an international consortium for advanced AI risk evaluations, discuss issues regarding its implementation, discuss lessons that can be learnt from previous international institutions and existing proposals for international AI governance institutions, and, finally, we recommend concrete steps to advance the establishment of the proposed consortium: (i) solicit feedback from stakeholders, (ii) conduct additional research, (iii) conduct a workshop(s) for stakeholders, (iv) analyze feedback and create final proposal, (v) solicit funding, and (vi) create a consortium., Comment: 50 pages, 2 figures; updated w/ a few minor revisions based on feedback from SoLaR Workshop reviewers (on 5 page version)

Multi-agent influence diagrams (MAIDs) are a popular game-theoretic model based on Bayesian networks. In some settings, MAIDs offer significant advantages over extensive-form game representations. Previous work on MAIDs has assumed that agents employ behavioural policies, which set independent conditional probability distributions over actions for each of their decisions. In settings with imperfect recall, however, a Nash equilibrium in behavioural policies may not exist. We overcome this by showing how to solve MAIDs with forgetful and absent-minded agents using mixed policies and two types of correlated equilibrium. We also analyse the computational complexity of key decision problems in MAIDs, and explore tractable cases. Finally, we describe applications of MAIDs to Markov games and team situations, where imperfect recall is often unavoidable., Comment: In Proceedings TARK 2023, arXiv:2307.04005

This article provides a proactive functional assessment and intervention framework for addressing challenging behaviors in young children. A three-tiered model is described that outlines prevention on the primary, secondary, and tertiary levels and remediation strategies that may be used to ameliorate challenging behaviors demonstrated by young children. (Contains references.) (Author/CR)

EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led and NSF co-funded field campaign that will provide critical information for quantifying the export and fate of upper ocean net primary production (NPP) using satellite information and state of the art technology.

Particle cycling rates in marine systems are difficult to measure directly, but of great interest in understanding how carbon and other elements are distributed throughout the ocean. Here, rates of particle production, aggregation, disaggregation, sinking, remineralization, and transport mediated by zooplankton diel vertical migration were estimated from size-fractionated measurements of particulate organic carbon (POC) concentration collected during the NASA EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) cruise at Station P in summer 2018. POC data were combined with a particle cycling model using an inverse method. Our estimates of the total POC settling flux throughout the water column are consistent with those derived from thorium-234 disequilibrium and sediment traps. A budget for POC in two size fractions, small (1–51 µm) and large (> 51 µm), was produced for both the euphotic zone (0–100 m) and the upper mesopelagic zone (100–500 m). We estimated that POC export at the base of the euphotic zone was 2.2 ± 0.8 mmol m−2 d−1, and that both small and large particles contributed considerably to the total export flux along the water column. The model results indicated that throughout the upper 500 m, remineralization leads to a larger loss of small POC than does aggregation, whereas disaggregation results in a larger loss of large POC than does remineralization. Of the processes explicitly represented in the model, zooplankton diel vertical migration is a larger source of large POC to the upper mesopelagic zone than the convergence of large POC due to particle sinking. Positive model residuals reveal an even larger unidentified source of large POC in the upper mesopelagic zone. Overall, our posterior estimates of particle cycling rate constants do not deviate much from values reported in the literature, i.e., size-fractionated POC concentration data collected at Station P are largely consistent with prior estimates given their uncertainties. Our budget

The field of plastic surgery, formally organized in 1931 with the founding of the American Society of Plastic and Reconstructive Surgery, was shaped in many ways by a small practice of Philadelphia physicians. At the center of the practice was Warren B. Davis, a Philadelphia otolaryngologist and plastics pioneer whose innovations in cleft palate surgery would lead to significant improvements in functional and cosmetic outcomes in his time. In addition to his own innovations, Davis was responsible for the training of John Reese, the inventor of the Reese dermatome that changed the face of burn medicine during World War II. Aside from his contributions to surgery and the founding of the American Society of Plastic and Reconstructive Surgery, Dr. Davis was also the founder and first editor of the Plastic and Reconstructive Surgery journal which to this day is the premiere, authoritative journal of plastic surgery. Lastly, Dr. Davis established a plastic surgical practice, now Jefferson Plastic Surgery. Unique in its longevity, this practice would continue to shape the field of plastic surgery and continues to improve lives today—109 years after its founding in 1913.

Training reinforcement learning (RL) agents using scalar reward signals is often infeasible when an environment has sparse and non-Markovian rewards. Moreover, handcrafting these reward functions before training is prone to misspecification, especially when the environment's dynamics are only partially known. This paper proposes a novel pipeline for learning non-Markovian task specifications as succinct finite-state `task automata' from episodes of agent experience within unknown environments. We leverage two key algorithmic insights. First, we learn a product MDP, a model composed of the specification's automaton and the environment's MDP (both initially unknown), by treating the product MDP as a partially observable MDP and using the well-known Baum-Welch algorithm for learning hidden Markov models. Second, we propose a novel method for distilling the task automaton (assumed to be a deterministic finite automaton) from the learnt product MDP. Our learnt task automaton enables the decomposition of a task into its constituent sub-tasks, which improves the rate at which an RL agent can later synthesise an optimal policy. It also provides an interpretable encoding of high-level environmental and task features, so a human can readily verify that the agent has learnt coherent tasks with no misspecifications. In addition, we take steps towards ensuring that the learnt automaton is environment-agnostic, making it well-suited for use in transfer learning. Finally, we provide experimental results compared with two baselines to illustrate our algorithm's performance in different environments and tasks., Comment: 14 pages, 7 figures, Accepted to the 26th European Conference on Artificial Intelligence (ECAI 2023)

© 2019 Elsevier B.V. Escherichia coli encoding colibactin (clb), cytolethal distending toxin (cdt), and hemolysin-associated cytotoxic necrotizing factor (cnf) are associated with various intestinal and extra-intestinal diseases in humans and animals. Small mammal pets are not evaluated for genotoxin-encoding E. coli. Thus, the prevalence of such strains is unknown. The objective of this study was to isolate and characterize genotoxin-encoding E. coli from healthy and ill small mammal pets examined at a veterinary clinic and at two animal adoption centers. E. coli isolates were cultured from fecal samples and biochemically characterized. A total of 65 animals, including mice, rats, rabbits, guinea pigs, and hedgehogs, were screened. Twenty-six E. coli isolates were obtained from 24 animals. Twelve of the 26 isolates (46.2 %) were PCR-positive for the pks genes clbA and clbQ. Two isolates (7.7 %) were PCR-positive for cnf. All isolates were PCR-negative for cdt. All genotoxin-encoding isolates belonged to the pathogen-associated phylogenetic group B2. Representative genotoxin-encoding isolates had serotypes previously associated with clinical disease in humans and animals. Isolates encoding pks or cnf induced megalocytosis and cytotoxicity to HeLa cells in vitro. Although most isolates were obtained from healthy pets, two guinea pigs with diarrhea had pks-positive isolates cultured from their feces. Whole genome sequencing on four representative isolates confirmed the presence of pks and cnf genes and identified other virulence factors associated with pathogenicity in animals and humans. Our results suggest that small mammalian pets may serve as a reservoir for potentially pathogenic E. coli and implicate a zoonotic risk.

Chronic inflammation of the colon causes genomic and/or transcriptomic events, which can lead to expression of non-canonical protein sequences contributing to oncogenesis. To better understand these mechanisms, Rag2−/−Il10−/− mice were infected with Helicobacter hepaticus to induce chronic inflammation of the cecum and the colon. Transcriptomic data from harvested proximal colon samples were used to generate a customized FASTA database containing non-canonical protein sequences. Using a proteogenomic approach, mass spectrometry data for proximal colon proteins were searched against this custom FASTA database using the Galaxy for Proteomics (Galaxy-P) platform. In addition to the increased abundance in inflammatory response proteins, we also discovered several non-canonical peptide sequences derived from unique proteoforms. We confirmed the veracity of these novel sequences using an automated bioinformatics verification workflow with targeted MS-based assays for peptide validation. Our bioinformatics discovery workflow identified 235 putative non-canonical peptide sequences, of which 58 were verified with high confidence and 39 were validated in targeted proteomics assays. This study provides insights into challenges faced when identifying non-canonical peptides using a proteogenomics approach and demonstrates an integrated workflow addressing these challenges. Our bioinformatic discovery and verification workflow is publicly available and accessible via the Galaxy platform and should be valuable in non-canonical peptide identification using proteogenomics.

Background The gut microbiome is altered in patients with inflammatory bowel disease, yet how these alterations contribute to intestinal inflammation is poorly understood. Murine models have demonstrated the importance of the microbiome in colitis since colitis fails to develop in many genetically susceptible animal models when re-derived into germ-free environments. We have previously shown that Wiskott-Aldrich syndrome protein (WASP)-deficient mice (Was−/−) develop spontaneous colitis, similar to human patients with loss-of-function mutations in WAS. Furthermore, we showed that the development of colitis in Was−/− mice is Helicobacter dependent. Here, we utilized a reductionist model coupled with multi-omics approaches to study the role of host-microbe interactions in intestinal inflammation. Results Was−/− mice colonized with both altered Schaedler flora (ASF) and Helicobacter developed colitis, while those colonized with either ASF or Helicobacter alone did not. In Was−/− mice, Helicobacter relative abundance was positively correlated with fecal lipocalin-2 (LCN2), a marker of intestinal inflammation. In contrast, WT mice colonized with ASF and Helicobacter were free of inflammation and strikingly, Helicobacter relative abundance was negatively correlated with LCN2. In Was−/− colons, bacteria breach the mucus layer, and the mucosal relative abundance of ASF457 Mucispirillum schaedleri was positively correlated with fecal LCN2. Meta-transcriptomic analyses revealed that ASF457 had higher expression of genes predicted to enhance fitness and immunogenicity in Was−/− compared to WT mice. In contrast, ASF519 Parabacteroides goldsteinii’s relative abundance was negatively correlated with LCN2 in Was−/− mice, and transcriptional analyses showed lower expression of genes predicted to facilitate stress adaptation by ASF519 in Was−/−compared to WT mice. Conclusions These studies indicate that the effect of a microbe on the immune system can be context dependent

© 2021, The Author(s). Cyclomodulins are virulence factors that modulate cellular differentiation, apoptosis, and proliferation. These include colibactin (pks), cytotoxic necrotizing factor (cnf), and cytolethal distending toxin (cdt). Pathogenic pks+, cnf+, and cdt+ E. coli strains are associated with inflammatory bowel disease (IBD) and colorectal cancer in humans and animals. Captive marmosets are frequently afflicted with IBD-like disease, and its association with cyclomodulins is unknown. Cyclomodulin-encoding E. coli rectal isolates were characterized using PCR-based assays in healthy and clinically affected marmosets originating from three different captive sources. 139 E. coli isolates were cultured from 122 of 143 marmosets. The pks gene was detected in 56 isolates (40%), cnf in 47 isolates (34%), and cdt in 1 isolate (0.7%). The prevalences of pks+ and cnf+ E. coli isolates were significantly different between the three marmoset colonies. 98% of cyclomodulin-positive E. coli belonged to phylogenetic group B2. Representative isolates demonstrated cyclomodulin cytotoxicity, and serotyping and whole genome sequencing were consistent with pathogenic E. coli strains. However, the presence of pks+, cnf+, or cdt+ E. coli did not correlate with clinical gastrointestinal disease in marmosets. Cyclomodulin-encoding E. coli colonize laboratory common marmosets in a manner dependent on the source, potentially impacting reproducibility in marmoset models.

© 2020 The Authors. The gut microbiome is the largest source of intrinsic non-self-antigens that are continuously sensed by the immune system but typically do not elicit lymphocyte responses. CD4+ T cells are critical to sustain uninterrupted tolerance to microbial antigens and to prevent intestinal inflammation. However, clinical interventions targeting commensal bacteria-specific CD4+ T cells are rare, because only a very limited number of commensal-derived epitopes have been identified. Here, we used a new approach to study epitopes and identify T cell receptors expressed by CD4+Foxp3+ (Treg) cells specific for commensal-derived antigens. Using this approach, we found that antigens from Akkermansia muciniphila reprogram naïve CD4+ T cells to the Treg lineage, expand preexisting microbe specific Tregs, and limit wasting disease in the CD4+ T cell transfer model of colitis. These data suggest that the administration of specific commensal epitopes may help to widen the repertoire of specific Tregs that control intestinal inflammation.

Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.

Gastric helicobacters (Helicobacter (H.) pylori and non-H. pylori Helicobacter species (NHPHs)) colonize the stomach of humans and/or animals. Helicobacter species identification is essential since many of them are recognized as human and/or animal pathogens. Currently, Helicobacter species can only be differentiated using molecular methods. Differentiation between NHPHs using MALDI-TOF MS has not been described before, probably because these species are poorly represented in current MALDI-TOF MS databases. Therefore, we identified 93 gastric Helicobacter isolates of 10 different Helicobacter species using MALDI-TOF MS in order to establish a more elaborate Helicobacter reference database. While the MALDI Biotyper database was not able to correctly identify any of the isolates, the in-house database correctly identified all individual mass spectra and resulted in 82% correct species identification based on the two highest log score matches (with log scores ≥2). In addition, a dendrogram was constructed using all newly created main spectrum profiles. Nine main clusters were formed, with some phylogenetically closely related Helicobacter species clustering closely together and well-defined subclusters being observed in specific species. Current results suggest that MALDI-TOF MS allows rapid differentiation between gastric Helicobacter species, provided that an extensive database is at hand and variation due to growth conditions and agar-medium-related peaks are taken into account.

© 2020, © 2020 Taylor & Francis Group, LLC. Infection with Helicobacter pylori causes chronic inflammation and is a risk factor for gastric cancer. Antibiotic treatment or increased dietary folate prevents gastric carcinogenesis in male INS-GAS mice. To determine potential synergistic effects, H. pylori-infected male INS-GAS mice were fed an amino acid defined (AAD) diet with increased folate and were treated with antibiotics after 18 weeks of H. pylori infection. Antibiotic therapy decreased gastric pathology, but dietary folate had no effect. However, the combination of antibiotics and the AAD diet induced anemia, gastric hemorrhage, and mortality. Clinical presentation suggested hypovitaminosis K potentially caused by dietary deficiency and dysbiosis. Based on current dietary guidelines, the AAD diet was deficient in vitamin K. Phylloquinone administered subcutaneously and via a reformulated diet led to clinical improvement with no subsequent mortalities and increased hepatic vitamin K levels. We characterized the microbiome and menaquinone profiles of antibiotic-treated and antibiotic-free mice. Antibiotic treatment decreased the abundance of menaquinone producers within orders Bacteroidales and Verrucomicrobiales. PICRUSt predicted decreases in canonical menaquinone biosynthesis genes, menA and menD. Reduction of menA from Akkermansia muciniphila, Bacteroides uniformis, and Muribaculum intestinale were confirmed in antibiotic-treated mice. The fecal menaquinone profile of antibiotic-treated mice had reduced MK5 and MK6 and increased MK7 and MK11 compared to antibiotic-free mice. Loss of menaquinone-producing microbes due to antibiotics altered the enteric production of vitamin K. This study highlights the role of diet and the microbiome in maintaining vitamin K homeostasis.

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Recent reports suggest that the East Asian liver fluke infection, caused by Opisthorchis viverrini, which is implicated in opisthorchiasis-associated cholangiocarcinoma, serves as a reservoir of Helicobacter pylori. The opisthorchiasis-affected cholangiocytes that line the intrahepatic biliary tract are considered to be the cell of origin of this malignancy. Here, we investigated interactions in vitro among human cholangiocytes, Helicobacter pylori strain NCTC 11637, and the congeneric bacillus, Helicobacter bilis. Exposure to increasing numbers of H. pylori at 0, 1, 10, 100 bacilli per cholangiocyte of the H69 cell line induced phenotypic changes including the profusion of thread-like filopodia and a loss of cell-cell contact, in a dose-dependent fashion. In parallel, following exposure to H. pylori, changes were evident in levels of mRNA expression of epithelial to mesenchymal transition (EMT)-encoding factors including snail, slug, vimentin, matrix metalloprotease, zinc finger E-box-binding homeobox, and the cancer stem cell marker CD44. Analysis to quantify cellular proliferation, migration, and invasion in real-time by both H69 cholangiocytes and CC-LP-1 line of cholangiocarcinoma cells using the xCELLigence approach and Matrigel matrix revealed that exposure to ≥10 H. pylori bacilli per cell stimulated migration and invasion by the cholangiocytes. In addition, 10 bacilli of H. pylori stimulated contact-independent colony establishment in soft agar. These findings support the hypothesis that infection by H. pylori contributes to the malignant transformation of the biliary epithelium.

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.

© 2020, Society for Mucosal Immunology. Mice deficient in the IL-10 pathway are the most widely used models of intestinal immunopathology. IL-17A is strongly implicated in gut disease in mice and humans, but conflicting evidence has drawn IL-17’s role in the gut into question. IL-22 regulates antimicrobial and repair activities of intestinal epithelial cells (IECs) and is closely associated with IL-17A responses but it’s role in chronic disease is uncertain. We report that IL-22, like IL-17A, is aberrantly expressed in colitic Il10−/− mice. While IL-22+Th17 cells were elevated in the colon, IL-22-producing ILC3s were highly enriched in the small intestines of Il10−/− mice. Remarkably, Il10−/−Il22−/− mice did not develop colitis despite retaining high levels of Th17 cells and remaining colonized with colitogenic Helicobacter spp. Accordant with IL-22-induced IEC proliferation, the epithelia hyperplasia observed in Il10−/− animals was reversed in Il10−/−Il22−/− mice. Also, the high levels of antimicrobial IL-22-target genes, including Reg3g, were normalized in Il10−/−Il22−/− mice. Consistent with a heightened antimicrobial environment, Il10−/− mice had reduced diversity of the fecal microbiome that was reestablished in Il10−/−Il22−/− animals. These data suggest that spontaneous colitis in Il10−/− mice is driven by IL-22 and implicates an underappreciated IL-10/IL-22 axis in regulating intestinal homeostasis.

© 2020 Background: Colombians in coastal Tumaco have a lower incidence of Helicobacter pylori-associated gastric cancer compared to individuals from Tuquerres in the high Andes. This is despite nearly universal prevalence of H. pylori infection and chronic gastritis. Methods: H. pylori infection was confirmed by Steiner stain and serology using African and European-origin strains. Gastric histology and serum inflammatory biomarkers in dyspeptic Tumaco or Tuquerres patients were evaluated to predict progression of gastric lesions. Results: H. pylori infection was nearly universal by Steiner stain and serology. IgG response to European-origin H. pylori strains were greater than African-origin. High gastric cancer-risk Tuquerres patients, compared to low-risk Tumaco, had significant odds ratios for lesion progression associated with serum IL-5, trefoil factor 3 (TFF3), and low pepsinogen I/II ratio. Sensitivity and specificity for these parameters was 63.8% and 67.9%, respectively, with correctly classifying patients at 66.7%. Most odds ratios for 26 other biomarkers were significant for the town of residency, indicating an environmental impact on Tumaco patients associated with decreased lesion progression. Conclusion: An IL-5 association with progression of gastric lesions is novel and could be evaluated in addition to TFF3 and pepsinogen I/II ratio as a non-invasive prognostic screen. Results suggest Tumaco patients were exposed to infectious diseases beyond H. pylori such as the documented high incidence of helminthiasis and toxoplasmosis. Impact: Results support a prior recommendation to evaluate TFF3 and pepsinogen I/II together to predict aggressive gastric histology. Our data indicate IL-5 should be further evaluated as prognostic parameter.

© 2020 The Authors Background & Aims: Tight junctions form a barrier to the paracellular passage of luminal antigens. Although most tight junction proteins reside within the apical tight junction complex, claudin-18 localizes mainly to the basolateral membrane where its contribution to paracellular ion transport is undefined. Claudin-18 loss in mice results in gastric neoplasia development and tumorigenesis that may or may not be due to tight junction dysfunction. The aim here was to investigate paracellular permeability defects in stomach mucosa from claudin-18 knockout (Cldn18-KO) mice. Methods: Stomach tissue from wild-type, heterozygous, or Cldn18-KO mice were stripped of the external muscle layer and mounted in Ussing chambers. Transepithelial resistance, dextran 4 kDa flux, and potential difference (PD) were calculated from the chambered tissues after identifying differences in tissue histopathology that were used to normalize these measurements. Marker expression for claudins and ion transporters were investigated by transcriptomic and immunostaining analysis. Results: No paracellular permeability defects were evident in stomach mucosa from Cldn18-KO mice. RNAseq identified changes in 4 claudins from Cldn18–KO mice, particularly the up-regulation of claudin-2. Although claudin-2 localized to tight junctions in cells at the base of gastric glands, its presence did not contribute overall to mucosal permeability. Stomach tissue from Cldn18–KO mice also had no PD versus a lumen-negative PD in tissues from wild-type mice. This difference resulted from changes in transcellular Cl– permeability with the down-regulation of Cl– loading and Cl– secreting anion transporters. Conclusions: Our findings suggest that Cldn18-KO has no effect on tight junction permeability in the stomach from adult mice but rather affects anion permeability. The phenotype in these mice may thus be secondary to transcellular anion transporter expression/function in the absence of claudin-18.

Argues that using functional behavioral assessment (FBA) to identify individual factors that may be contributing to a student's behavior problem and building a positive behavioral-intervention plan will produce effective disciplinary practices. Components of successful implementation of FBA and overarching challenges to the use of FBA are discussed. (CR)

Examines likely changes in the roles and responsibilities of public school personnel from the implementation of disciplinary provisions of the 1997 Amendments to the Individuals with Disabilities Education Act. Also addresses implementing functional behavioral assessments and behavioral intervention plans, and provides guidelines for implementing the disciplinary provisions. (CR)

Predicated on the idea that many scholars will come into contact with the media during the course of their careers, this guide addresses the "rules of the game" for academics when dealing with the media. The guide demystifies the workings of the press and other media and offers concrete, practical advice on how to work effectively with the media. Topics discussed in the guide include: giving news interviews to print, television, and radio reporters; writing op/ed pieces; appearing on television talk shows; and working with and through university public relations offices. The guide concludes with a list of several "reasonable expectations" for academics dealing with the media. (NKA)

The oceans teem with heterotrophic bacterioplankton that play an appreciable role in the uptake of dissolved organic carbon (DOC) derived from phytoplankton net primary production (NPP). As such, bacterioplankton carbon demand (BCD), or gross heterotrophic production, represents a major carbon pathway that influences the seasonal accumulation of DOC in the surface ocean and, subsequently, the potential vertical or horizontal export of seasonally accumulated DOC. Here, we examine the contributions of bacterioplankton and DOM to ecological and biogeochemical carbon flow pathways, including those of the microbial loop and the biological carbon pump, in the Western North Atlantic Ocean (∼39-54°N along ∼40°W) over a composite annual phytoplankton bloom cycle. Combining field observations with data collected from corresponding DOC remineralization experiments, we estimate the efficiency at which bacterioplankton utilize DOC, demonstrate seasonality in the fraction of NPP that supports BCD, and provide evidence for shifts in the bioavailability and persistence of the seasonally accumulated DOC. Our results indicate that while the portion of DOC flux through bacterioplankton relative to NPP increased as seasons transitioned from high to low productivity, there was a fraction of the DOM production that accumulated and persisted. This persistent DOM is potentially an important pool of organic carbon available for export to the deep ocean via convective mixing, thus representing an important export term of the biological carbon pump.

We recovered 12 archival geolocators deployed on Eastern Kingbirds (Tvrannus tyrannus) breeding in New York (NY; n = 3, 2 with 2 years of data), Nebraska (NE; n = 6, 1 with 2 years of data), and Oregon (OR; n = 3) to describe migratory routes, timing and rates of migration, nonbreeding season distributions, and migratory connectedness. NY fall migrants migrated along the Atlantic coast to Florida, flew either nonstop across the Gulf of Mexico (GoM; 2 of 3 birds) or stopped once along the way (Cuba and Cayman Islands in different years) to land in Yucatan/Central America. Fall birds from NE and OR arrived at the GoM in the region of the border between Texas and Louisiana, and most likely took a land route to Central America In spring, all NY birds flew nonstop across the GoM, and once in North America, took a more inland mute than in fall. Trans-GoM flights were more common among NE and OR birds in spring than fall. Birds migrated faster in spring than fall, and in both seasons, late departure was associated with more rapid migration. Migratory connectivity was low, and all birds from OR, and one bird from NE and NY each, occupied a single region in northwestern Amazonia (southern Colombia, northern Peru, and eastern Ecuador) while in South America. Most kingbirds from NE and NY were intratropical migrants, occupying 2 regions for periods of >= 30 d. The latter birds migrated farther south to western Brazil and northern Bolivia, but then moved north to later use the same area in northwestern Amazonia where other birds remained throughout the overwinter period. Northwestern Amazonia thus appears to be a critical area for all Eastern Kingbirds during the nonbreeding season, possibly because a prolonged wet season supports abundant fruit resources.

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Siegel, D. A., Cetinic, I., Graff, J. R., Lee, C. M., Nelson, N., Perry, M. J., Ramos, I. S., Steinberg, D. K., Buesseler, K., Hamme, R., Fassbender, A. J., Nicholson, D., Omand, M. M., Robert, M., Thompson, A., Amaral, V., Behrenfeld, M., Benitez-Nelson, C., Bisson, K., Boss, E., Boyd, P. W., Brzezinski, M., Buck, K., Burd, A., Burns, S., Caprara, S., Carlson, C., Cassar, N., Close, H. H., D’Asaro, E., Durkin, C., Erickson, Z., Estapa, M. L., Fields, E., Fox, J., Freeman, S., Gifford, S., Gong, W., Gray, D., Guidi, L., Haëntjens, N., Halsey, K., Huot, Y., Hansell, D., Jenkins, B., Karp-Boss, L., Kramer, S., Lam, P., Lee, J-M., Maas, A., Marchal, O., Marchetti, A., McDonnell, A., McNair, H., Menden-Deuer, S., Morison, F., Niebergall, A. K., Passow, U., Popp, B., Potvin, G., Resplandy, L., Roca-Martí, M., Roesler, C., Rynearson, T., Traylor, S., Santoro, A., Seraphin, K. D., Sosik, H. M., Stamieszkin, K., Stephens, B., Tang, W., Van Mooy, B., Xiong, Y., Zhang, X. An operational overview of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) Northeast Pacific field deployment. Elementa: Science of the Anthropocene, 9(1), (2021): 1, https://doi.org/10.1525/elementa.2020.00107., The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work, DAS, NN, KB, EF, SK, AB, AM, UP: NASA 80NSSC17K0692. MJB, EB, JG, LG, KH, LKB, JF, NH: NASA 80NSSC17K0568. KB, CBN, LR, MRM: NASA 80NSSC17K0555. CC, DH, BS: NASA 80NSSC18K0437. HC: NSF 1830016. BP, KDS: NSF 1829425. ME, KB, CD, MO: NASA 80NSSC17K0662. AF: NSF 1756932. BJ, KB, MB, SB, SC: NSF 1756442. PH, OM, JML: NSF 1829614. CL, ED, DN, MO, MJP, AT, ZN, ST: NASA 80NSSC17K0663. AM, NC, SG, WT, AN, WG: NASA 80NSSC17K0552. SMD, TR, HM, FM: NASA 80NSSC17K0716. CR, HS: NASA 80NSSC17K0700. AS, PB: NASA 80NSSC18K1431. DS, AM, KS NASA 80NSSC17K0654. BVM: NSF 1756254. XZ, DG, LG, YH: NASA 80NSSC17K0656 and 80NSSC20K0350.

EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led and NSF co-funded field campaign that will provide critical information for quantifying the export and fate of upper ocean net primary production (NPP) using satellite information and state of the art technology.

© 2020, The Author(s). Manuka honey (MH) is currently used as a wound treatment and suggested to be effective in Methicillin-resistant Staphylococcus aureus (MRSA) elimination. We sought to optimize the synthesis of MH microneedles (MHMs) while maintaining the MH therapeutic effects. MHMs were synthesized using multiple methods and evaluated with in vitro assays. MHMs demonstrated excellent bactericidal activity against MRSA at concentrations ≥ 10% of honey, with vacuum-prepared honey appearing to be the most bactericidal, killing bacterial concentrations as high as 8 × 107 CFU/mL. The wound-healing assay demonstrated that, at concentrations of 0.1%, while the cooked honey had incomplete wound closure, the vacuum-treated honey trended towards faster wound closure. In this study, we demonstrate that the method of MHM synthesis is crucial to maintaining MH properties. We optimized the synthesis of MHMs and demonstrated their potential utility in the treatment of MRSA infections as well as in wound healing. This is the first report of using MH as a substrate for the formation of dissolvable microneedles. This data supports the need for further exploration of this new approach in a wound-healing model and opens the door for the future use of MH as a component of microneedle scaffolds., NIH (Grants P30-ES002109 (JGF), P50-GM021700)

© 2020, © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group, on behalf of Shanghai Shangyixun Cultural Communication Co., Ltd. Inclusion body nephropathy (IBN) and kidney fibrosis in aged immunodeficient mice and, to lesser extent, in immunocompetent mice have been recently linked to infection of mouse kidney parvovirus (MKPV), also known as murine chapparvovirus (MuCPV). Knowledge about its prevalence and the complete genome sequence of more MKPV strains is essential for understanding phylogenetic relationships and pathogenicity among MKPV strains. In the present study using PCR and genome walking, we determined the complete 4440-nucleotide genome of a new MKPV strain, namely MIT-WI1, which was identified in IBN-affected Il2rg-/-Rag2-/- c-Kit W-sh/W-sh mice housed in the vivarium at Whitehead Institute for Biomedical Research (WI). The overall nucleotide (>94%) and deduced amino acid sequences (>98%) of p10, p15, NS1 (replicase), NS2 and VP1 (capsid protein) within the MIT-WI1 genome, are closely related to MKPV/MuCPV strains described in laboratory and wild Mus musculus mice. In addition, PCR and qPCR assays using newly designed primers conserved among the known MKPV/MuCPV genomes were developed and utilized to assess MKPV status in selected mice. MKPV was also detected in immunodeficient (NSG) and immunocompetent (Crl:CD1(ICR), UTXflox) mouse strains/stocks. The abundance of the MKPV genome copies was significantly correlated with the severity of IBN. Our data indicate that MKPV is present in selected mouse strains/stocks, and provides new insights into the genome evolution of MKPV., NIH (Grant P30-ES002109)

© Copyright © 2020 Batac, Miller, Moriarty, Shen, Fox and Ottemann. Southern sea otters (Enhydra lutris nereis) are threatened marine mustelids that commonly have gastric ulcers with secondary hemorrhage (melena) as a contributing cause of death. Although Helicobacter spp. infections are known to cause gastric ulcers and gastritis in humans and ferrets, it is unknown if the sea otter bacterium, H. enhydrae sp. nov., causes similar gastric pathology. Determining whether Helicobacter detection is associated with sea otter gastric pathology is the first step toward using this information to expedite diagnosis and treatment. We investigated the proportion of Helicobacter infections in 46 necropsied southern sea otters via quantitative real-time polymerase chain reaction (qPCR) of the 16S rRNA gene. Helicobacter DNA was detected in fresh-frozen and formalin-fixed gastric body and pyloric tissues using Helicobacter genus-specific 16S rRNA primers. Data from gross necropsy and histopathology were analyzed for associations between Helicobacter detection via qPCR and presence/absence of gastric pathology. ETEST® gradient strips were utilized to investigate antimicrobial minimum inhibitory concentrations for H. enhydrae isolates. Helicobacter spp. were detected in the gastric tissue of 85% of sea otters in this study. Fresh-frozen samples were more commonly Helicobacter qPCR-positive than formalin-fixed tissue, indicating variable sensitivity of detection in relation to post-necropsy tissue processing methods. Diagnosis of gastric ulcers at necropsy was significantly associated with Helicobacter qPCR detection in gastric mucosa (P = 0.005), while age, sex, presence of melena, shark trauma, and protozoal infection were not associated (P > 0.1). Helicobacter enhydrae isolates were sensitive to clarithromycin and tetracycline in vitro at physiologically relevant concentrations. Overall, this work suggests that Helicobacter spp. might be commonly found in southern sea otters, par

Recent reports suggest that the East Asian liver fluke infection, caused by Opisthorchis viverrini, which is implicated in opisthorchiasis-associated cholangiocarcinoma, serves as a reservoir of Helicobacter pylori. The opisthorchiasis-affected cholangiocytes that line the intrahepatic biliary tract are considered to be the cell of origin of this malignancy. Here, we investigated interactions in vitro among human cholangiocytes, Helicobacter pylori strain NCTC 11637, and the congeneric bacillus, Helicobacter bilis. Exposure to increasing numbers of H. pylori at 0, 1, 10, 100 bacilli per cholangiocyte of the H69 cell line induced phenotypic changes including the profusion of thread-like filopodia and a loss of cell-cell contact, in a dose-dependent fashion. In parallel, following exposure to H. pylori, changes were evident in levels of mRNA expression of epithelial to mesenchymal transition (EMT)-encoding factors including snail, slug, vimentin, matrix metalloprotease, zinc finger E-box-binding homeobox, and the cancer stem cell marker CD44. Analysis to quantify cellular proliferation, migration, and invasion in real-time by both H69 cholangiocytes and CC-LP-1 line of cholangiocarcinoma cells using the xCELLigence approach and Matrigel matrix revealed that exposure to ≥10 H. pylori bacilli per cell stimulated migration and invasion by the cholangiocytes. In addition, 10 bacilli of H. pylori stimulated contact-independent colony establishment in soft agar. These findings support the hypothesis that infection by H.pylori contributes to the malignant transformation of the biliary epithelium.

© 2020, The Author(s). Manuka honey (MH) is currently used as a wound treatment and suggested to be effective in Methicillin-resistant Staphylococcus aureus (MRSA) elimination. We sought to optimize the synthesis of MH microneedles (MHMs) while maintaining the MH therapeutic effects. MHMs were synthesized using multiple methods and evaluated with in vitro assays. MHMs demonstrated excellent bactericidal activity against MRSA at concentrations ≥ 10% of honey, with vacuum-prepared honey appearing to be the most bactericidal, killing bacterial concentrations as high as 8 × 107 CFU/mL. The wound-healing assay demonstrated that, at concentrations of 0.1%, while the cooked honey had incomplete wound closure, the vacuum-treated honey trended towards faster wound closure. In this study, we demonstrate that the method of MHM synthesis is crucial to maintaining MH properties. We optimized the synthesis of MHMs and demonstrated their potential utility in the treatment of MRSA infections as well as in wound healing. This is the first report of using MH as a substrate for the formation of dissolvable microneedles. This data supports the need for further exploration of this new approach in a wound-healing model and opens the door for the future use of MH as a component of microneedle scaffolds.

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Recent reports suggest that the East Asian liver fluke infection, caused by Opisthorchis viverrini, which is implicated in opisthorchiasis-associated cholangiocarcinoma, serves as a reservoir of Helicobacter pylori. The opisthorchiasis-affected cholangiocytes that line the intrahepatic biliary tract are considered to be the cell of origin of this malignancy. Here, we investigated interactions in vitro among human cholangiocytes, Helicobacter pylori strain NCTC 11637, and the congeneric bacillus, Helicobacter bilis. Exposure to increasing numbers of H. pylori at 0, 1, 10, 100 bacilli per cholangiocyte of the H69 cell line induced phenotypic changes including the profusion of thread-like filopodia and a loss of cell-cell contact, in a dose-dependent fashion. In parallel, following exposure to H. pylori, changes were evident in levels of mRNA expression of epithelial to mesenchymal transition (EMT)-encoding factors including snail, slug, vimentin, matrix metalloprotease, zinc finger E-box-binding homeobox, and the cancer stem cell marker CD44. Analysis to quantify cellular proliferation, migration, and invasion in real-time by both H69 cholangiocytes and CC-LP-1 line of cholangiocarcinoma cells using the xCELLigence approach and Matrigel matrix revealed that exposure to ≥10 H. pylori bacilli per cell stimulated migration and invasion by the cholangiocytes. In addition, 10 bacilli of H. pylori stimulated contact-independent colony establishment in soft agar. These findings support the hypothesis that infection by H. pylori contributes to the malignant transformation of the biliary epithelium.

Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.

© 2021, The Author(s). Cyclomodulins are virulence factors that modulate cellular differentiation, apoptosis, and proliferation. These include colibactin (pks), cytotoxic necrotizing factor (cnf), and cytolethal distending toxin (cdt). Pathogenic pks+, cnf+, and cdt+ E. coli strains are associated with inflammatory bowel disease (IBD) and colorectal cancer in humans and animals. Captive marmosets are frequently afflicted with IBD-like disease, and its association with cyclomodulins is unknown. Cyclomodulin-encoding E. coli rectal isolates were characterized using PCR-based assays in healthy and clinically affected marmosets originating from three different captive sources. 139 E. coli isolates were cultured from 122 of 143 marmosets. The pks gene was detected in 56 isolates (40%), cnf in 47 isolates (34%), and cdt in 1 isolate (0.7%). The prevalences of pks+ and cnf+ E. coli isolates were significantly different between the three marmoset colonies. 98% of cyclomodulin-positive E. coli belonged to phylogenetic group B2. Representative isolates demonstrated cyclomodulin cytotoxicity, and serotyping and whole genome sequencing were consistent with pathogenic E. coli strains. However, the presence of pks+, cnf+, or cdt+ E. coli did not correlate with clinical gastrointestinal disease in marmosets. Cyclomodulin-encoding E. coli colonize laboratory common marmosets in a manner dependent on the source, potentially impacting reproducibility in marmoset models.

© Copyright © 2020 Batac, Miller, Moriarty, Shen, Fox and Ottemann. Southern sea otters (Enhydra lutris nereis) are threatened marine mustelids that commonly have gastric ulcers with secondary hemorrhage (melena) as a contributing cause of death. Although Helicobacter spp. infections are known to cause gastric ulcers and gastritis in humans and ferrets, it is unknown if the sea otter bacterium, H. enhydrae sp. nov., causes similar gastric pathology. Determining whether Helicobacter detection is associated with sea otter gastric pathology is the first step toward using this information to expedite diagnosis and treatment. We investigated the proportion of Helicobacter infections in 46 necropsied southern sea otters via quantitative real-time polymerase chain reaction (qPCR) of the 16S rRNA gene. Helicobacter DNA was detected in fresh-frozen and formalin-fixed gastric body and pyloric tissues using Helicobacter genus-specific 16S rRNA primers. Data from gross necropsy and histopathology were analyzed for associations between Helicobacter detection via qPCR and presence/absence of gastric pathology. ETEST® gradient strips were utilized to investigate antimicrobial minimum inhibitory concentrations for H. enhydrae isolates. Helicobacter spp. were detected in the gastric tissue of 85% of sea otters in this study. Fresh-frozen samples were more commonly Helicobacter qPCR-positive than formalin-fixed tissue, indicating variable sensitivity of detection in relation to post-necropsy tissue processing methods. Diagnosis of gastric ulcers at necropsy was significantly associated with Helicobacter qPCR detection in gastric mucosa (P = 0.005), while age, sex, presence of melena, shark trauma, and protozoal infection were not associated (P > 0.1). Helicobacter enhydrae isolates were sensitive to clarithromycin and tetracycline in vitro at physiologically relevant concentrations. Overall, this work suggests that Helicobacter spp. might be commonly found in southern sea otters, par