Statistical inference of transmission fidelity of DNA methylation patterns over somatic cell divisions in mammals

We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation patterns with each pattern coming from a single cell and represented as an unordered pair of binary strings. The data are technically difficult and time-consuming to collect, putting a premium on an efficient inference method. Our aim is to estimate rates for the maintenance and de novo methylation events that gave rise to the observed patterns, while accounting for measurement error. We model data at multiple sites jointly, thus using whole-strand information, and considerably reduce confounding between parameters. We also adopt a hierarchical structure that allows for variation in rates across sites without an explosion in the effective number of parameters. Our context-specific priors capture the expected stationarity, or near-stationarity, of the stochastic process that generated the data analyzed here. This expected stationarity is shown to greatly increase the precision of the estimation. Applying our model to a data set collected at the human FMR1 locus, we find that measurement errors, generally ignored in similar studies, occur at a nontrivial rate (inappropriate bisulfite conversion error: 1.6$$ with 80$$ CI: 0.9--2.3$$). Accounting for these errors has a substantial impact on estimates of key biological parameters. The estimated average failure of maintenance rate and daughter de novo rate decline from 0.04 to 0.024 and from 0.14 to 0.07, respectively, when errors are accounted for. Our results also provide evidence that de novo events may occur on both parent and daughter strands: the median parent and daughter de novo rates are 0.08 (80$$ CI: 0.04--0.13) and 0.07 (80$$ CI: 0.04--0.11), respectively.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS297 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Evaluating an unconfined aquifer by analysis of age-dating tracers in stream water

The mean transit time (MTT) is a fundamental property of a groundwater flow system that is strongly related to the ratio of recharge rate to storage volume. However, obtaining samples for estimating the MTT using environmental tracers is problematic as flow-weighted samples over the full spectrum of transit times are needed. Samples collected fromthe base flow of a gaining stream in the North Carolina Coastal Plain (West Bear Creek) that were corrected for exchange with the atmosphere yielded environmental tracer concentrations (SF6 and CFC-11) very similar to flow-weighted values from nine or ten streambed piezometers that directly sampled groundwater during low streamflow. At higher streamflow on the falling limb of the hydrograph, stream tracer concentrations (after correction for gas exchange) were significantly higher than the flow-weighted mean from piezometers, consistent with dominance of the streamtracer signal by transient influx of surface water and/or younger subsurface water. The apparent MTT derived from SF6 in low flow stream water samples was 26 years, suggesting a groundwater recharge rate of about 210 mm/yr, that is consistent with vertical profiles obtained by sampling nested piezometers in the aquifer. When sampled under low flow conditions when streamflow consists of a high component of groundwater discharge, West Bear Creek appears to act as a flow-weighted integrator of transit times and, streamflow samples can provide fundamental information regarding groundwater recharge rate and MTT. Our study suggests that watershed-scale evaluation of some groundwater flow systems is possible without utilizing monitoring wells

STAR: Secret sharing for private threshold aggregation reporting

Threshold aggregation reporting systems promise a practical, privacy-preserving solution for developers to learn how their applications are used in-the-wild. Unfortunately, proposed systems to date prove impractical for wide scale adoption, suffering from a combination of requiring: i) prohibitive trust assumptions; ii) high computation costs; or iii) massive user bases. As a result, adoption of truly-private approaches has been limited to only a small number of enormous (and enormously costly) projects. In this work, we improve the state of private data collection by proposing STAR, a highly efficient, easily deployable system for providing cryptographically-enforced κ-anonymity protections on user data collection. The STAR protocol is easy to implement and cheap to run, all while providing privacy properties similar to, or exceeding the current state-of-the-art. Measurements of our open-source implementation of STAR find that it is 1773x quicker, requires 62.4x less communication, and is 24x cheaper to run than the existing state-of-the-art

Groundwater transit time distribution and mean from streambed sampling in an agricultural coastal plain watershed, North Carolina, USA

We measured groundwater apparent age (s) and seepage rate (v) in a sandy streambed using point-scale sampling and seepage blankets (a novel seepage meter). We found very similar MTT estimates from streambed point sampling in a 58 m reach (29 years) and a 2.5 km reach (31 years). The TTD for groundwater discharging to the stream was best fit by a gamma distribution model and was very similar for streambed point sampling in both reaches. Between adjacent point-scale and seepage blanket samples, water from the seepage blankets was generally younger, largely because blanket samples contained a fraction of ‘‘young’’ stream water. Correcting blanket data for the stream water fraction brought s estimates for most blanket samples closer to those for adjacent point samples. The MTT estimates from corrected blanket data were in good agreement with those from sampling streambed points adjacent to the blankets. Collectively, agreement among age-dating tracers, general accord between tracer data and piston-flow model curves, and large groundwater age gradients in the streambed, suggested that the piston flow apparent ages were reasonable estimates of the groundwater transit times for most samples. Overall, our results from two field campaigns suggest that groundwater collected in the streambed can provide reasonable estimates of apparent age of groundwater discharge, and that MTT can be determined from different agedating tracers and by sampling with different groundwater collection devices. Coupled streambed point measurements of groundwater age and groundwater seepage rate represent a novel, reproducible, and effective approach to estimating aquifer TTD and MTT

A comparative genomics multitool for scientific discovery and conservation

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity

Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways

To better understand the innate immune response to Vibrio cholerae infection, we tracked gene expression in the duodenal mucosa of 11 Bangladeshi adults with cholera, using biopsy specimens obtained immediately after rehydration and 30 and 180 days later. We identified differentially expressed genes and performed an analysis to predict differentially regulated pathways and upstream regulators. During acute cholera, there was a broad increase in the expression of genes associated with innate immunity, including activation of the NF-kappaB, mitogen-activated protein kinase (MAPK), and Toll-like receptor (TLR)-mediated signaling pathways, which, unexpectedly, persisted even 30 days after infection. Focusing on early differences in gene expression, we identified 37 genes that were differentially expressed on days 2 and 30 across the 11 participants. These genes included the endosomal Toll-like receptor gene TLR8, which was expressed in lamina propria cells. Underscoring a potential role for endosomal TLR-mediated signaling in vivo, our pathway analysis found that interferon regulatory factor 7 and beta 1 and alpha 2 interferons were among the top upstream regulators activated during cholera. Among the innate immune effectors, we found that the gene for DUOX2, an NADPH oxidase involved in the maintenance of intestinal homeostasis, was upregulated in intestinal epithelial cells during cholera. Notably, the observed increases in DUOX2 and TLR8 expression were also modeled in vitro when Caco-2 or THP-1 cells, respectively, were stimulated with live V. cholerae but not with heat-killed organisms or cholera toxin alone. These previously unidentified features of the innate immune response to V. cholerae extend our understanding of the mucosal immune signaling pathways and effectors activated in vivo following cholera

Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways

To better understand the innate immune response to Vibrio cholerae infection, we tracked gene expression in the duodenal mucosa of 11 Bangladeshi adults with cholera, using biopsy specimens obtained immediately after rehydration and 30 and 180 days later. We identified differentially expressed genes and performed an analysis to predict differentially regulated pathways and upstream regulators. During acute cholera, there was a broad increase in the expression of genes associated with innate immunity, including activation of the NF-kappaB, mitogen-activated protein kinase (MAPK), and Toll-like receptor (TLR)-mediated signaling pathways, which, unexpectedly, persisted even 30 days after infection. Focusing on early differences in gene expression, we identified 37 genes that were differentially expressed on days 2 and 30 across the 11 participants. These genes included the endosomal Toll-like receptor gene TLR8, which was expressed in lamina propria cells. Underscoring a potential role for endosomal TLR-mediated signaling in vivo, our pathway analysis found that interferon regulatory factor 7 and beta 1 and alpha 2 interferons were among the top upstream regulators activated during cholera. Among the innate immune effectors, we found that the gene for DUOX2, an NADPH oxidase involved in the maintenance of intestinal homeostasis, was upregulated in intestinal epithelial cells during cholera. Notably, the observed increases in DUOX2 and TLR8 expression were also modeled in vitro when Caco-2 or THP-1 cells, respectively, were stimulated with live V. cholerae but not with heat-killed organisms or cholera toxin alone. These previously unidentified features of the innate immune response to V. cholerae extend our understanding of the mucosal immune signaling pathways and effectors activated in vivo following cholera

Quantifying the fate of agricultural nitrogen in an unconfined aquifer: Stream-based observations at three measurement scales

We compared three stream-based sampling methods to study the fate of nitrate in groundwater in a coastal plain watershed: point measurements beneath the streambed, seepage blankets (novel seepage-meter design), and reach mass-balance. The methods gave similar mean groundwater seepage rates into the stream (0.3–0.6 m/d) during two 3–4 day field campaigns despite an order of magnitude difference in stream discharge between the campaigns. At low flow, estimates of flowweighted mean nitrate concentrations in groundwater discharge ([NO-3 ]FWM) and nitrate flux from groundwater to the stream decreased with increasing degree of channel influence and measurement scale, i.e., [NO-3 ]FWM was 654, 561, and 451 mM for point, blanket, and reach mass-balance sampling, respectively. At high flow the trend was reversed, likely because reach mass-balance captured inputs from shallow transient high-nitrate flow paths while point and blanket measurements did not. Point sampling may be better suited to estimating aquifer discharge of nitrate, while reach mass-balance reflects full nitrate inputs into the channel (which at high flow may be more than aquifer discharge due to transient flow paths, and at low flow may be less than aquifer discharge due to channel-based nitrate removal). Modeling dissolved N2 from streambed samples suggested (1) about half of groundwater nitrate was denitrified prior to discharge from the aquifer, and (2) both extent of denitrification and initial nitrate concentration in groundwater (700–1300 mM) were related to land use, suggesting these forms of streambed sampling for groundwater can reveal watershed spatial relations relevant to nitrate contamination and fate in the aquifer

Combining Citizen Science and Genomics to Investigate Tick, Pathogen, and Commensal Microbiome at Single-Tick Resolution

The prevalence of tickborne diseases worldwide is increasing virtually unchecked due to the lack of effective control strategies. The transmission dynamics of tickborne pathogens are influenced by the tick microbiome, tick co-infection with other pathogens, and environmental features. Understanding this complex system could lead to new strategies for pathogen control, but will require large-scale, high-resolution data. Here, we introduce Project Acari, a citizen science-based project to assay, at single-tick resolution, species, pathogen infection status, microbiome profile, and environmental conditions of tens of thousands of ticks collected from numerous sites across the United States. In the first phase of the project, we collected more than 2,400 ticks wild-caught by citizen scientists and developed high-throughput methods to process and sequence them individually. Applying these methods to 192 Ixodes scapularis ticks collected in a region with a high incidence of Lyme disease, we found that 62% were colonized by Borrelia burgdorferi, the Lyme disease pathogen. In contrast to previous reports, we did not find an association between the microbiome diversity of a tick and its probability of carrying B. burgdorferi. However, we did find undescribed associations between B. burgdorferi carriage and the presence of specific microbial taxa within individual ticks. Our findings underscore the power of coupling citizen science with high-throughput processing to reveal pathogen dynamics. Our approach can be extended for massively parallel screening of individual ticks, offering a powerful tool to elucidate the ecology of tickborne disease and to guide pathogen-control initiatives