Integrating NHANES and toxicity forecaster data to compare pesticide exposure and bioactivity by farmwork history and US citizenship.

BACKGROUND: Farmworkers in the United States, especially migrant workers, face unique barriers to healthcare and have documented disparities in health outcomes. Exposure to pesticides, especially those persistent in the environment, may contribute to these health disparities. OBJECTIVE: Quantify differences in pesticide exposure bioactivity by farmworker category and US citizenship status. METHODS: We queried the National Health and Nutrition Examination Study (NHANES) from 1999-2014 for pesticide exposure biomarker concentrations among farmworkers and non-farmworkers by citizenship status. We combined this with toxicity assay data from the US Environmental Protection Agency's (EPA's) Toxicity Forecaster (ToxCast). We estimated adverse biological effects that occur across a range of human population-relevant pesticide doses. RESULTS: In total, there were 844 people with any farmwork history and 23,592 non-farmworkers. Of 12 commonly detectable pesticide biomarkers in NHANES, 2,4-dichlorophenoxyacetic acid (OR = 3.76, p = 1.33 × 10-6) was significantly higher in farmworkers than non-farmworkers. Farmworkers were 1.15 times more likely to have a bioactive pesticide biomarker measurement in comparison to non-farmworkers (adjusted OR = 1.15, 95% CI: 0.87, 1.51). Non-U.S. citizens were 1.39 times more likely to have bioactive pesticide biomarker concentrations compared to people with U.S. citizenship (adjusted OR 1.39, 95% CI: 1.17, 1.64). Additionally, non-citizens were significantly more exposed to bioactive levels of ß-hexachlorocyclohexane (BHC) (OR = 8.10, p = 1.33 × 10-6), p,p-DDE (OR = 2.60, p = 0.02), and p,p'-DDT (OR = 7.75, p = 0.01). IMPACT STATEMENT: Farmworkers are a vulnerable population due to social determinants of health and occupational exposures. Here, we integrate US population chemical biomonitoring data and toxicity outcome data to assess pesticide exposure by farmwork history and citizenship. We find that farmworkers and those without US citizenship are significantly more likely to be exposed to concentrations of pesticides which are bioactive in toxicological assays. Thus, farmworkers employed in the US but who are not citizens could be at increased risk of harm to their health due to pesticides. These findings are important to shape evidence-based policies in regulatory science to promote worker safety.

Integrating NHANES and Toxicity Forecaster Data to Compare Pesticide Exposure and Bioactivity by Farmwork History and US Citizenship.

Introduction: Farmworkers in the United States, especially migrant workers, face unique barriers to healthcare and have documented disparities in health outcomes. Exposure to pesticides, especially those persistent in the environment, may contribute to these health disparities. Methods: We queried the National Health and Nutrition Examination Study (NHANES) from 1999-2014 for pesticide exposure biomarker concentrations among farmworkers and non-farmworkers by citizenship status. We combined this with toxicity assay data from the US Environmental Protection Agency's (EPA's) Toxicity Forecast Dashboard (ToxCast). We estimated adverse biological effects that occur across a range of human population-relevant pesticide doses. Results: In total, there were 1,137 people with any farmwork history and 20,205 non-farmworkers. Of the 14 commonly detectable pesticide biomarkers in NHANES, 2,4-dichlorophenol (OR= 4.32, p= 2.01×10 -7 ) was significantly higher in farmworkers than non-farmworkers. Farmworkers were 1.37 times more likely to have a bioactive pesticide biomarker measurement in comparison to non-farmworkers (adjusted OR=1.37, 95% CI: 1.10, 1.71). Within farmworkers only, those without U.S. citizenships were 1.31 times more likely to have bioactive pesticide biomarker concentrations compared those with U.S. citizenship (adjusted OR 1.31, 95% CI: 0.75, 2.30). Additionally, non-citizen farmworkers were significantly more exposed to bioactive levels of ß -hexachlorocyclohexane (BHC) (OR= 8.50, p= 1.23×10 -9 ), p,p-DDE (OR= 2.98, p= 3.11×10 -3 ), and p,p'-DDT (OR= 10.78, p= 8.70×10 -4 ). Discussion: These results highlight pesticide exposure disparities in farmworkers, particularly those without U.S. citizenship. Many of these exposures are occurring at doses which are bioactive in toxicological assays.

Corrigendum: Spatial Organization and Recruitment of Non-Specific T Cells May Limit T Cell-Macrophage Interactions Within Mycobacterium tuberculosis Granulomas.

[This corrects the article DOI: 10.3389/fimmu.2020.613638.].

Risk factors for increased COVID-19 case-fatality in the United States: A county-level analysis during the first wave.

The ongoing COVID-19 pandemic is causing significant morbidity and mortality across the US. In this ecological study, we identified county-level variables associated with the COVID-19 case-fatality rate (CFR) using publicly available datasets and a negative binomial generalized linear model. Variables associated with decreased CFR included a greater number of hospitals per 10,000 people, banning religious gatherings, a higher percentage of people living in mobile homes, and a higher percentage of uninsured people. Variables associated with increased CFR included a higher percentage of the population over age 65, a higher percentage of Black or African Americans, a higher asthma prevalence, and a greater number of hospitals in a county. By identifying factors that are associated with COVID-19 CFR in US counties, we hope to help officials target public health interventions and healthcare resources to locations that are at increased risk of COVID-19 fatalities.

To Sobol or not to Sobol? The effects of sampling schemes in systems biology applications.

Computational and mathematical models in biology rely heavily on the parameters that characterize them. However, robust estimates for their values are typically elusive and thus a large parameter space becomes necessary for model study, particularly to make translationally impactful predictions. Sampling schemes exploring parameter spaces for models are used for a variety of purposes in systems biology, including model calibration and sensitivity analysis. Typically, random sampling is used; however, when models have a high number of unknown parameters or the models are highly complex, computational cost becomes an important factor. This issue can be reduced through the use of efficient sampling schemes such as Latin hypercube sampling (LHS) and Sobol sequences. In this work, we compare and contrast three sampling schemes - random sampling, LHS, and Sobol sequences - for the purposes of performing both parameter sensitivity analysis and model calibration. In addition, we apply these analyses to different types of computational and mathematical models of varying complexity: a simple ODE model, a complex ODE model, and an agent-based model. In general, the sampling scheme had little effect when used for calibration efforts, but when applied to sensitivity analyses, Sobol sequences exhibited faster convergence. While the observed benefit to convergence is relatively small, Sobol sequences are computationally less expensive to compute than LHS samples and also have the benefit of being deterministic, which allows for better reproducibility of results.

Risk factors for increased COVID-19 case-fatality in the United States: A county-level analysis during the first wave.

The ongoing COVID-19 pandemic is causing significant morbidity and mortality across the US. In this ecological study, we identified county-level variables associated with the COVID-19 case-fatality rate (CFR) using publicly available datasets and a negative binomial generalized linear model. Variables associated with decreased CFR included a greater number of hospitals per 10,000 people, banning religious gatherings, a higher percentage of people living in mobile homes, and a higher percentage of uninsured people. Variables associated with increased CFR included a higher percentage of the population over age 65, a higher percentage of Black or African Americans, a higher asthma prevalence, and a greater number of hospitals in a county. By identifying factors that are associated with COVID-19 CFR in US counties, we hope to help officials target public health interventions and healthcare resources to locations that are at increased risk of COVID-19 fatalities.

Male fetal sex affects uteroplacental angiogenesis in growth restriction mouse model†.

Abnormally increased angiotensin II activity related to maternal angiotensinogen (AGT) genetic variants, or aberrant receptor activation, is associated with small-for-gestational-age babies and abnormal uterine spiral artery remodeling in humans. Our group studies a murine AGT gene titration transgenic (TG; 3-copies of the AGT gene) model, which has a 20% increase in AGT expression mimicking a common human AGT genetic variant (A[-6]G) associated with intrauterine growth restriction (IUGR) and spiral artery pathology. We hypothesized that aberrant maternal AGT expression impacts pregnancy-induced uterine spiral artery angiogenesis in this mouse model leading to IUGR. We controlled for fetal sex and fetal genotype (e.g., only 2-copy wild-type [WT] progeny from WT and TG dams were included). Uteroplacental samples from WT and TG dams from early (days 6.5 and 8.5), mid (d12.5), and late (d16.5) gestation were studied to assess uterine natural killer (uNK) cell phenotypes, decidual metrial triangle angiogenic factors, placental growth and capillary density, placental transcriptomics, and placental nutrient transport. Spiral artery architecture was evaluated at day 16.5 by contrast-perfused three-dimensional microcomputed tomography (3D microCT). Our results suggest that uteroplacental angiogenesis is significantly reduced in TG dams at day 16.5. Males from TG dams are associated with significantly reduced uteroplacental angiogenesis from early to late gestation compared with their female littermates and WT controls. Angiogenesis was not different between fetal sexes from WT dams. We conclude that male fetal sex compounds the pathologic impact of maternal genotype in this mouse model of growth restriction.

The GRE in Public Health Admissions: Barriers, Waivers, and Moving Forward.

In the wake of COVID-19, there is an urgent need for a diverse public health work force to address problems presented or exacerbated by the global pandemic. Educational programs that create our work force both train and shape the makeup of access through graduate applications. The Graduate Record Exam has a number of standing issues, with additional barriers created by the pandemic. We trace the GRE waiver movement over several years, focusing on the gradual adoption in CEPH accredited programs and the rapid expansion of temporary waivers as a response to testing access. Going forward, we need to consider gaps in waivers during the pandemic and how this data can be used to shape our future use of the GRE.

Modulation of Bacterial Fitness and Virulence Through Antisense RNAs.

Regulatory RNAs contribute to gene expression control in bacteria. Antisense RNAs (asRNA) are a class of regulatory RNAs that are transcribed from opposite strands of their target genes. Typically, these untranslated transcripts bind to cognate mRNAs and rapidly regulate gene expression at the post-transcriptional level. In this article, we review asRNAs that modulate bacterial fitness and increase virulence. We chose examples that underscore the variety observed in nature including, plasmid- and chromosome-encoded asRNAs, a riboswitch-regulated asRNA, and asRNAs that require other RNAs or RNA-binding proteins for stability and activity. We explore how asRNAs improve bacterial fitness and virulence by modulating plasmid acquisition and maintenance, regulating transposon mobility, increasing resistance against bacteriophages, controlling flagellar production, and regulating nutrient acquisition. We conclude with a brief discussion on how this knowledge is helping to inform current efforts to develop new therapeutics.

Spatial Organization and Recruitment of Non-Specific T Cells May Limit T Cell-Macrophage Interactions Within Mycobacterium tuberculosis Granulomas.

Tuberculosis (TB) is a worldwide health problem; successful interventions such as vaccines and treatment require a 2better understanding of the immune response to infection with Mycobacterium tuberculosis (Mtb). In many infectious diseases, pathogen-specific T cells that are recruited to infection sites are highly responsive and clear infection. Yet in the case of infection with Mtb, most individuals are unable to clear infection leading to either an asymptomatically controlled latent infection (the majority) or active disease (roughly 5%-10% of infections). The hallmark of Mtb infection is the recruitment of immune cells to lungs leading to development of multiple lung granulomas. Non-human primate models of TB indicate that on average <10% of T cells within granulomas are Mtb-responsive in terms of cytokine production. The reason for this reduced responsiveness is unknown and it may be at the core of why humans typically are unable to clear Mtb infection. There are a number of hypotheses as to why this reduced responsiveness may occur, including T cell exhaustion, direct downregulation of antigen presentation by Mtb within infected macrophages, the spatial organization of the granuloma itself, and/or recruitment of non-Mtb-specific T cells to lungs. We use a systems biology approach pairing data and modeling to dissect three of these hypotheses. We find that the structural organization of granulomas as well as recruitment of non-specific T cells likely contribute to reduced responsiveness.

Vancomycin-Resistant Enterococcus Acquisition in a Tertiary Care Hospital: Testing the Roles of Antibiotic Use, Proton Pump Inhibitor Use, and Colonization Pressure.

BACKGROUND: Vancomycin-resistant Enterococcus (VRE) is a leading cause of healthcare-associated infections, and asymptomatic colonization precedes infection. VRE continues to spread despite widespread application of pathogen-specific control guidelines. A better understanding of the risk factors for transmission is needed. METHODS: A retrospective matched case-control study was performed from June 2013 through December 2016 in a single institution. Patients in 6 intensive care units, 1 hematology and oncology unit, and 1 bone marrow transplant unit were screened by means of rectal swab sampling on admission and weekly thereafter. Case patients had a negative swab sample followed by a positive sample >3 days after admission. Controls were closely matched to case patients based on time from admission to the second swab sample, unit in which the second sample was obtained, and date of admission. Comorbidity data, procedures, healthcare settings and exposures, culture data, and duration of antibiotic and proton pump inhibitor (PPI) therapy were abstracted from the electronic medical record. A multivariable risk factor model for conversion was generated using purposeful selection. RESULTS: A total of 551 case patients were matched with controls. The largest modifiable effects on VRE acquisition were ≥1 day of vancomycin therapy (odd ratio, 1.98; P < .001), ≥1 day of aerobic antibiotic therapy (1.90; P < .001), and a dose-dependent effect of PPI therapy (odds ratio per day of therapy, 1.09; P < .001). Colonization pressures from patients identified to be carriers and placed in contact precautions did not confer increased risk. CONCLUSIONS: Decreasing PPI use and preventing the inappropriate initiation of antibiotic therapy are modifiable targets to decrease VRE transmission in the hospital.

LytTR Regulatory Systems: A potential new class of prokaryotic sensory system.

The most commonly studied prokaryotic sensory signal transduction systems include the one-component systems, phosphosignaling systems, extracytoplasmic function (ECF) sigma factor systems, and the various types of second messenger systems. Recently, we described the regulatory role of two separate sensory systems in Streptococcus mutans that jointly control bacteriocin gene expression, natural competence development, as well as a cell death pathway, yet they do not function via any of the currently recognized signal transduction paradigms. These systems, which we refer to as LytTR Regulatory Systems (LRS), minimally consist of two proteins, a transcription regulator from the LytTR Family and a transmembrane protein inhibitor of this transcription regulator. Here, we provide evidence suggesting that LRS are a unique uncharacterized class of prokaryotic sensory system. LRS exist in a basal inactive state. However, when LRS membrane inhibitor proteins are inactivated, an autoregulatory positive feedback loop is triggered due to LRS regulator protein interactions with direct repeat sequences located just upstream of the -35 sequences of LRS operon promoters. Uncharacterized LRS operons are widely encoded by a vast array of Gram positive and Gram negative bacteria as well as some archaea. These operons also contain unique direct repeat sequences immediately upstream of their operon promoters indicating that positive feedback autoregulation is a globally conserved feature of LRS. Despite the surprisingly widespread occurrence of LRS operons, the only characterized examples are those of S. mutans. Therefore, the current study provides a useful roadmap to investigate LRS function in the numerous other LRS-encoding organisms.

Correction: Accumulation and expression of horizontally acquired genes in Arcobacter cryaerophilus that thrives in sewage.

[This corrects the article DOI: 10.7717/peerj.3269.].

Dynamic balance of pro- and anti-inflammatory signals controls disease and limits pathology.

Immune responses to pathogens are complex and not well understood in many diseases, and this is especially true for infections by persistent pathogens. One mechanism that allows for long-term control of infection while also preventing an over-zealous inflammatory response from causing extensive tissue damage is for the immune system to balance pro- and anti-inflammatory cells and signals. This balance is dynamic and the immune system responds to cues from both host and pathogen, maintaining a steady state across multiple scales through continuous feedback. Identifying the signals, cells, cytokines, and other immune response factors that mediate this balance over time has been difficult using traditional research strategies. Computational modeling studies based on data from traditional systems can identify how this balance contributes to immunity. Here we provide evidence from both experimental and mathematical/computational studies to support the concept of a dynamic balance operating during persistent and other infection scenarios. We focus mainly on tuberculosis, currently the leading cause of death due to infectious disease in the world, and also provide evidence for other infections. A better understanding of the dynamically balanced immune response can help shape treatment strategies that utilize both drugs and host-directed therapies.

Intraperitoneal nanotherapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin.

Herein, we report an efficient combinatorial therapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin. DJ-1 protein modulates, either directly or indirectly, different oncogenic pathways that support and promote survival, growth, and invasion of ovarian cancer cells. To evaluate the potential of this novel therapy, we have engineered a cancer-targeted nanoplatform and validated that DJ-1 siRNA delivered by this nanoplatform after intraperitoneal injection efficiently downregulates the DJ-1 protein in metastatic ovarian cancer tumors and ascites. In vivo experiments revealed that DJ-1 siRNA monotherapy outperformed cisplatin alone by inhibiting tumor growth and increasing survival of mice with metastatic ovarian cancer. Finally, three cycles of siRNA-mediated DJ-1 therapy in combination with a low dose of cisplatin completely eradicated ovarian cancer tumors from the mice, and there was no cancer recurrence detected for the duration of the study, which lasted 35 weeks.

Whole-Genome Sequence of Coxiella burnetii Nine Mile RSA439 (Phase II, Clone 4), a Laboratory Workhorse Strain.

Here, we report the whole-genome sequence of Coxiella burnetii Nine Mile RSA439 (phase II, clone 4), a laboratory strain used extensively to investigate the biology of this intracellular bacterial pathogen. The genome consists of a 1.97-Mb chromosome and a 37.32-kb plasmid.

Horizontally Acquired Biosynthesis Genes Boost Coxiella burnetii's Physiology.

Coxiella burnetii, the etiologic agent of acute Q fever and chronic endocarditis, has a unique biphasic life cycle, which includes a metabolically active intracellular form that occupies a large lysosome-derived acidic vacuole. C. burnetii is the only bacterium known to thrive within such an hostile intracellular niche, and this ability is fundamental to its pathogenicity; however, very little is known about genes that facilitate Coxiella's intracellular growth. Recent studies indicate that C. burnetii evolved from a tick-associated ancestor and that the metabolic capabilities of C. burnetii are different from that of Coxiella-like bacteria found in ticks. Horizontally acquired genes that allow C. burnetii to infect and grow within mammalian cells likely facilitated the host shift; however, because of its obligate intracellular replication, C. burnetii would have lost most genes that have been rendered redundant due to the availability of metabolites within the host cell. Based on these observations, we reasoned that horizontally derived biosynthetic genes that have been retained in the reduced genome of C. burnetii are ideal candidates to begin to uncover its intracellular metabolic requirements. Our analyses identified a large number of putative foreign-origin genes in C. burnetii, including tRNAGlu2 that is potentially required for heme biosynthesis, and genes involved in the production of lipopolysaccharide-a virulence factor, and of critical metabolites such as fatty acids and biotin. In comparison to wild-type C. burnetii, a strain that lacks tRNAGlu2 exhibited reduced growth, indicating its importance to Coxiella's physiology. Additionally, by using chemical agents that block heme and biotin biosyntheses, we show that these pathways are promising targets for the development of new anti-Coxiella therapies.

Accumulation and expression of multiple antibiotic resistance genes in Arcobacter cryaerophilus that thrives in sewage.

We explored the bacterial diversity of untreated sewage influent samples of a wastewater treatment plant in Tucson, AZ and discovered that Arcobacter cryaerophilus, an emerging human pathogen of animal origin, was the most dominant bacterium. The other highly prevalent bacteria were members of the phyla Bacteroidetes and Firmicutes, which are major constituents of human gut microbiome, indicating that bacteria of human and animal origin intermingle in sewage. By assembling a near-complete genome of A. cryaerophilus, we show that the bacterium has accumulated a large number of antibiotic resistance genes (ARGs) probably enabling it to thrive in the wastewater. We also determined that a majority of ARGs was being expressed in sewage, suggestive of trace levels of antibiotics or other stresses that could act as a selective force that amplifies multidrug resistant bacteria in municipal sewage. Because all bacteria are not eliminated even after several rounds of wastewater treatment, ARGs in sewage could affect public health due to their potential to contaminate environmental water.

Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution.

Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination.

Friend or Foe-Light Availability Determines the Relationship between Mycorrhizal Fungi, Rhizobia and Lima Bean (Phaseolus lunatus L.).

Plant associations with root microbes represent some of the most important symbioses on earth. While often critically promoting plant fitness, nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) also demand significant carbohydrate allocation in exchange for key nutrients. Though plants may often compensate for carbon loss, constraints may arise under light limitation when plants cannot extensively increase photosynthesis. Under such conditions, costs for maintaining symbioses may outweigh benefits, turning mutualist microbes into parasites, resulting in reduced plant growth and reproduction. In natural systems plants commonly grow with different symbionts simultaneously which again may interact with each other. This might add complexity to the responses of such multipartite relationships. We experimented with lima bean (Phaseolus lunatus), which efficiently forms associations with both types of root symbionts. We applied full light and low-light to each of four treatments of microbial inoculation. After an incubation period of 14 weeks, we quantified vegetative aboveground and belowground biomass and number and viability of seeds to determine effects of combined inoculant and light treatment on plant fitness. Under light-limited conditions, vegetative and reproductive traits were inhibited in AMF and rhizobia inoculated lima bean plants relative to controls (un-colonized plants). Strikingly, reductions in seed production were most critical in combined treatments with rhizobia x AMF. Our findings suggest microbial root symbionts create additive costs resulting in decreased plant fitness under light-limited conditions.