Chromatin analysis of occluded genes

We recently described two opposing states of transcriptional competency. One is termed ‘competent’ whereby a gene is capable of responding to trans-acting transcription factors of the cell, such that it is active if appropriate transcriptional activators are present, though it can also be silent if activators are absent or repressors are present. The other is termed ‘occluded’ whereby a gene is silenced by cis-acting, chromatin-based mechanisms in a manner that blocks it from responding to trans-acting factors, such that it is silent even when activators are present in the cellular milieu. We proposed that gene occlusion is a mechanism by which differentiated cells stably maintain their phenotypic identities. Here, we describe chromatin analysis of occluded genes. We found that DNA methylation plays a causal role in maintaining occlusion for a subset of occluded genes. We further examined a variety of other chromatin marks typically associated with transcriptional silencing, including histone variants, covalent histone modifications and chromatin-associated proteins. Surprisingly, we found that although many of these marks are robustly linked to silent genes (which include both occluded genes and genes that are competent but silent), none is linked specifically to occluded genes. Although the observation does not rule out a possible causal role of these chromatin marks in occlusion, it does suggest that these marks might be secondary effect rather than primary cause of the silent state in many genes

Systematic identification of cis-silenced genes by trans complementation

A gene’s transcriptional output is the combined product of two inputs: diffusible factors in the cellular milieu acting in trans, and chromatin state acting in cis. Here, we describe a strategy for dissecting the relative contribution of cis versus trans mechanisms to gene regulation. Referred to as trans complementation, it entails fusing two disparate cell types and searching for genes differentially expressed between the two genomes of fused cells. Any differential expression can be causally attributed to cis mechanisms because the two genomes of fused cells share a single homogenized milieu in trans. This assay uncovered a state of transcriptional competency that we termed ‘occluded’ whereby affected genes are silenced by cis-acting mechanisms in a manner that blocks them from responding to the trans-acting milieu of the cell. Importantly, occluded genes in a given cell type tend to include master triggers of alternative cell fates. Furthermore, the occluded state is maintained during cell division and is extraordinarily stable under a wide range of physiological conditions. These results support the model that the occlusion of lineage-inappropriate genes is a key mechanism of cell fate restriction. The identification of occluded genes by our assay provides a hitherto unavailable functional readout of chromatin state that is distinct from and complementary to gene expression status

Deworming in pre-school age children: A global empirical analysis of health outcomes

<div><p>Background</p><p>There is debate over the effectiveness of deworming children against soil-transmitted helminthiasis (STH) to improve health outcomes, and current evidence may be limited in study design and generalizability. However, programmatic deworming continues throughout low and middle-income countries.</p><p>Methodology and principal findings</p><p>We performed an empirical evaluation of the relationship between deworming in pre-school age children (ages 1–4 years) within the previous 6 months, as proxy-reported by the mother, and health outcomes of weight, height, and hemoglobin. We used nationally representative cross-sectional data from 45 countries using the Demographic and Health Surveys (DHS) during the period 2005–2016. We used logistic regression with coarsened exact matching, fixed effects for survey and year, and person-level covariates. We included data on 325,115 children in 45 STH-endemic countries from 66 DHS surveys. Globally in STH-endemic countries, children who received deworming treatment were less likely to be stunted (1.2 percentage point decline from mean of 36%; 95% CI [-1.9, -0.5%]; p<0.001), but we did not detect consistent associations between deworming and anemia or weight. In sub-Saharan Africa, we found that children who received deworming treatment were less likely to be stunted (1.1 percentage point decline from mean of 36%; 95% CI [-2.1, -0.2%]; p = 0.01) and less likely to have anemia (1.8 percentage point decline from mean of 58%; 95% CI [-2.8, -0.7%]; p<0.001), but we did not detect consistent associations between deworming and weight. These findings were robust across multiple statistical models, and we did not find consistently measurable associations with data from non-endemic settings.</p><p>Conclusions and significance</p><p>Among pre-school age children, we detected a robust and consistent association between deworming and reduced stunting, with additional evidence for reduced anemia in sub-Saharan Africa. We did not find a consistent relationship between deworming and improved weight. This global empirical analysis provides evidence to support the deworming of pre-school age children.</p></div

Characteristics of pre-school age children stratified by receipt of deworming, unmatched and CEM matched groups.

<p>Characteristics of pre-school age children stratified by receipt of deworming, unmatched and CEM matched groups.</p

Regression model estimating the relationship in health outcomes for pre-school age children reported to have received treatment for intestinal worms in past 6 months.

<p>Regression model estimating the relationship in health outcomes for pre-school age children reported to have received treatment for intestinal worms in past 6 months.</p

Study countries and DHS survey year.

<p>Study countries and DHS survey year.</p

Design of a parallel cluster-randomized trial assessing the impact of a demand-side sanitation and hygiene intervention on sustained behavior change and mental well-being in rural and peri-urban Amhara, Ethiopia: Andilaye study protocol

Unimproved water, sanitation, and hygiene (WASH) behaviors are key drivers of infectious disease transmission and influencers of mental well-being. While WASH is seen as a critical enabler of health, important knowledge gaps related to the content and delivery of effective, holistic WASH programming exist. Corresponding impacts of WASH on mental well-being are also underexplored. There is a need for more robust implementation research that yields information regarding whether and how community-based, demand-side interventions facilitate progressive and sustained adoption of improved sanitation and hygiene behaviors and downstream health impacts. The purpose of this protocol is to detail the rationale and design of a cluster-randomized trial evaluating the impact of a demand-side sanitation and hygiene intervention on sustained behavior change and mental well-being in rural and peri-urban Amhara, Ethiopia.MethodsTogether with partners, we developed a theoretically-informed, evidence-based behavioral intervention called Andilaye. We randomly selected and assigned 50 sub-districts (kebeles) from three purposively selected districts (woredas)half to receive the Andilaye intervention, and half the standard of care sanitation and hygiene programming (i.e., community-led total sanitation and hygiene [CLTSH]). During baseline, midline, and endline, we will collect data on an array of behavioral factors, potential moderators (e.g., water and sanitation insecurity, collective efficacy), and our primary study outcomes: sanitation and hygiene behaviors and mental well-being. We will perform a process evaluation to assess intervention fidelity and related attributes.DiscussionWhile CLTSH has fostered sanitation and hygiene improvements in Ethiopia, evidence of behavioral slippage, or regression to unimproved practices in communities previously declared open defecation free exists. Other limitations of CLTSH, such as its focus on disgust, poor triggering, and over-saturation of Health Extension Workers have been documented. We employed rigorous formative research and practically applied social and behavioral theory to develop Andilaye, a scalable intervention designed to address these issues and complement existing service delivery within Ethiopia's Health Extension Program. Evidence from this trial may help address knowledge gaps related to scalable alternatives to CLTSH and inform sanitation and hygiene programming and policy in Ethiopia and beyond.Trial registrationThis trial was registered with clinicaltrials.gov (NCT03075436) on March 9, 2017

Spatial heterogeneity of neighborhood-level water and sanitation access in informal urban settlements: A cross-sectional case study in Beira, Mozambique.

Rapid urbanization, resulting in population growth within informal settlements, has worsened exclusion and inequality in access to water and sanitation (WASH) services in the poorest and most marginalized communities. In this study, we describe the heterogeneity in water service satisfaction and WASH access in low-income, peri-urban neighborhoods of Beira, Mozambique, and examine whether this heterogeneity can be explained by distance to water distribution mains. Using spatial statistics and regression analyses, we identify spatial heterogeneity in household WASH access, as well as consumer-reported satisfaction with water services (services, pressure, quality, and sufficient quantity). We find that as distance from the water main increased, both access to an improved water source at the household and satisfaction with water pressure decreases, and water supply intermittency increases, controlling for household density and socioeconomic status. The odds of a household having access to a water source at the household or on the compound decreases with every 100-meter increase in distance from a water main pipe (odds ratio [OR] 0.87, 95% confidence interval [CI]: 0.82, 0.92). Satisfaction with water services also decreases with every 100-meter increase in distance from a water main pipe (OR: 0.80; 95% CI: 0.69, 0.94). Days of availability in the past week decreases by a factor of 0.22 for every 100-meter increase in distance from the water main (95% CI: -0.29, -0.15). Findings from this study highlight the unequal household access to water and sanitation in urban informal settlements, even within low-income neighborhoods. Describing this heterogeneity of access to water services, sanitation, and satisfaction-and the factors influencing them-can inform stakeholders and guide the development of infrastructural solutions to reduce water access inequities within urban settings

The impact of a demand-side sanitation and hygiene promotion intervention on sustained behavior change and health in Amhara, Ethiopia: A cluster-randomized trial.

Behaviors related to water, sanitation, and hygiene (WASH) are key drivers of infectious disease transmission, and experiences of WASH are potential influencers of mental well-being. Important knowledge gaps exist related to the content and delivery of effective WASH programs and their associated health impacts, particularly within the contexts of government programs implemented at scale. We developed and tested a demand-side intervention called Andilaye, which aimed to change behaviors related to sanitation, personal hygiene, and household environmental sanitation. This theory-informed intervention was delivered through the existing Ethiopian Health Extension Programme (HEP). It was a multilevel intervention with a catalyzing event at the community level and behavior change activities at group and household levels. We randomly selected and assigned 50 kebeles (sub-districts) from three woredas (districts), half to receive the Andilaye intervention, and half the standard of care sanitation and hygiene programming (i.e., community-led total sanitation and hygiene [CLTSH]). We collected data on WASH access, behavioral outcomes, and mental well-being. A total of 1,589 households were enrolled into the study at baseline; 1,472 households (94%) participated in an endline assessment two years after baseline, and approximately 14 months after the initiation of a multi-level intervention. The intervention did not improve construction of latrines (prevalence ratio [PR]: 0.99; 95% CI: 0.82, 1.21) or handwashing stations with water (PR: 0.96; 95% CI: 0.72, 1.26), or the removal of animal feces from the compound (PR: 1.10; 95% CI: 0.95, 1.28). Nor did it impact anxiety (PR: 0.90; 95% CI: 0.72, 1.11), depression (PR: 0.83; 95% CI: 0.64, 1.07), emotional distress (PR: 0.86; 95% CI: 0.67, 1.09) or well-being (PR: 0.90; 95% CI: 0.74, 1.10) scores. We report limited impact of the intervention, as delivered, on changes in behavior and mental well-being. The effectiveness of the intervention was limited by poor intervention fidelity. While sanitation and hygiene improvements have been documented in Ethiopia, behavioral slippage, or regression to unimproved practices, in communities previously declared open defecation free is widespread. Evidence from this trial may help address knowledge gaps related to challenges associated with scalable alternatives to CLTSH and inform sanitation and hygiene programming and policy in Ethiopia and beyond. Trial registration: This trial was registered with clinicaltrials.gov (NCT03075436) on March 9, 2017