Placental transcriptome variation associated with season, location, and urinary prenatal pyrethroid metabolites of Thai farm-working women

Prenatal exposure to pyrethroids is linked to adverse health effects in early life and proper placental function is critical to fetal development. This study explores the impact of prenatal pyrethroid exposure, as well as factors impacting exposure and effect, on the placental transcriptome, to understand pyrethroid exposures' relationship to placental function. The study of Asian Women and their Offspring's Development and Environmental Exposures (SAWASDEE) recruited pregnant farm-working women from two agricultural districts in the Chiang Mai province of Thailand between 2017 and 2019. This cohort was predominantly exposed to cypermethrin (type II), alongside pyrethroids such as cyfluthrin (type II) and permethrin (type I). In 253 participants, maternal urinary pyrethroid metabolites, 3-phenoxybenzoic acid (PBA), cis-3-(2,2-Dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (CDCCA), and trans-3-(2,2-Dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid (TDCCA) were measured in early, middle, and late pregnancy and adjusted for urinary creatinine. The placental transcriptome was analyzed using RNA-Seq. Using generalized linear regression, we identified differentially expressed genes (DEGs) associated with the sum of each metabolite across pregnancy, as well as those associated with location of residence and season of birth. Pathway and upstream transcription factor analyses were performed to examine potential mechanisms associated with DEGs. Notably, TDCCA and CDCCA levels peaked in late pregnancy, with significant regional differences, particularly higher levels in the Fang region. Placental gene expression analysis showed no DEGs associated with individual metabolites at FDR<0.05. However, 251 DEGs by location, implicating immune response and oxidative phosphorylation pathways, were identified, while season of birth was associated with 2585 DEGs, over-represented in fibrosis signaling and metabolism pathways. Finally, transcription factor analysis identified 226 and 282 transcription factors associated with location and season, respectively, related to cell proliferation, differentiation, and the immune system. These alterations may have significant implications for fetal development and other pathologic processes, highlighting the importance of monitoring environmental exposures during pregnancy.

Placental microRNAs relate to early childhood growth trajectories

BACKGROUND

Poor placental function is a common cause of intrauterine growth restriction, which in turn is associated with increased risks of adverse health outcomes. Our prior work suggests that birthweight and childhood obesity-associated genetic variants functionally impact placental function and that placental microRNA are associated with birthweight. To address the influence of the placenta beyond birth, we assessed the relationship between placental microRNAs and early childhood growth.

METHODS

Using the SITAR package, we generated two parameters that describe individual weight trajectories of children (0-5 years) in the New Hampshire Birth Cohort Study (NHBCS, n = 238). Using negative binomial generalized linear models, we identified placental microRNAs that relate to growth parameters (FDR < 0.1), while accounting for sex, gestational age at birth, and maternal parity.

RESULTS

Genes targeted by the six growth trajectory-associated microRNAs are enriched (FDR < 0.05) in growth factor signaling (TGF/beta: miR-876; EGF/R: miR-155, Let-7c; FGF/R: miR-155; IGF/R: Let-7c, miR-155), calmodulin signaling (miR-216a), and NOTCH signaling (miR-629).

CONCLUSIONS

Growth-trajectory microRNAs target pathways affecting placental proliferation, differentiation and function. Our results suggest a role for microRNAs in regulating placental cellular dynamics and supports the Developmental Origins of Health and Disease hypothesis that fetal environment can have impacts beyond birth.

IMPACT

We found that growth trajectory associated placenta microRNAs target genes involved in signaling pathways central to the formation, maintenance and function of placenta; suggesting that placental cellular dynamics remain critical to infant growth to term and are under the control of microRNAs. Our results contribute to the existing body of research suggesting that the placenta plays a key role in programming health in the offspring. This is the first study to relate molecular patterns in placenta, specifically microRNAs, to early childhood growth trajectory.

Analysis of Pregnancy Complications and Epigenetic Gestational Age of Newborns

Importance

Preeclampsia, gestational hypertension, and gestational diabetes, the most common pregnancy complications, are associated with substantial morbidity and mortality in mothers and children. Little is known about the biological processes that link the occurrence of these pregnancy complications with adverse child outcomes; altered biological aging of the growing fetus up to birth is one molecular pathway of increasing interest.

Objective

To evaluate whether exposure to each of these 3 pregnancy complications (gestational diabetes, gestational hypertension, and preeclampsia) is associated with accelerated or decelerated gestational biological age in children at birth.

Design, Setting, and Participants

Children included in these analyses were born between 1998 and 2018 and spanned multiple geographic areas of the US. Pregnancy complication information was obtained from maternal self-report and/or medical record data. DNA methylation measures were obtained from blood biospecimens collected from offspring at birth. The study used data from the national Environmental Influences on Child Health Outcomes (ECHO) multisite cohort study collected and recorded as of the August 31, 2021, data lock date. Data analysis was performed from September 2021 to December 2022.

Exposures

Three pregnancy conditions were examined: gestational hypertension, preeclampsia, and gestational diabetes.

Main Outcomes and Measures

Accelerated or decelerated biological gestational age at birth, estimated using existing epigenetic gestational age clock algorithms.

Results

A total of 1801 child participants (880 male [48.9%]; median [range] chronological gestational age at birth, 39 [30-43] weeks) from 12 ECHO cohorts met the analytic inclusion criteria. Reported races included Asian (49 participants [2.7%]), Black (390 participants [21.7%]), White (1026 participants [57.0%]), and other races (92 participants [5.1%]) (ie, American Indian or Alaska Native, Native Hawaiian or other Pacific Islander, multiple races, and other race not specified). In total, 524 participants (29.0%) reported Hispanic ethnicity. Maternal ages ranged from 16 to 45 years of age with a median of 29 in the analytic sample. A range of maternal education levels, from less than high school (260 participants [14.4%]) to Bachelor's degree and above (629 participants [34.9%]), were reported. In adjusted regression models, prenatal exposure to maternal gestational diabetes (β, -0.423; 95% CI, -0.709 to -0.138) and preeclampsia (β, -0.513; 95% CI, -0.857 to -0.170), but not gestational hypertension (β, 0.003; 95% CI, -0.338 to 0.344), were associated with decelerated epigenetic aging among exposed neonates vs those who were unexposed. Modification of these associations, by sex, was observed with exposure to preeclampsia (β, -0.700; 95% CI, -1.189 to -0.210) and gestational diabetes (β, -0.636; 95% CI, -1.070 to -0.200), with associations observed among female but not male participants.

Conclusions and Relevance

This US cohort study of neonate biological changes related to exposure to maternal pregnancy conditions found evidence that preeclampsia and gestational diabetes delay biological maturity, especially in female offspring.

Variation in placental microRNA expression associates with maternal family history of cardiovascular disease

In the United States, cardiovascular disease is the leading cause of death and the rate of maternal mortality remains among the highest of any industrialized nation. Maternal cardiometabolic health throughout gestation and postpartum is representative of placental health and physiology. Both proper placental functionality and placental microRNA expression are essential to successful pregnancy outcomes, and both are highly sensitive to genetic and environmental sources of variation. Placental pathologies, such as preeclampsia, are associated with maternal cardiovascular health but may also contribute to the developmental programming of chronic disease in offspring. However, the role of more subtle alterations to placental function and microRNA expression in this developmental programming remains poorly understood. We performed small RNA sequencing to investigate microRNA in placentae from the Rhode Island Child Health Study (n = 230). MicroRNA counts were modeled on maternal family history of cardiovascular disease using negative binomial generalized linear models. MicroRNAs were considered to be differentially expressed at a false discovery rate (FDR) less than 0.10. Parallel mRNA sequencing data and bioinformatic target prediction software were then used to identify potential mRNA targets of differentially expressed microRNAs. Nine differentially expressed microRNAs were identified (FDR < 0.1). Bioinformatic target prediction revealed 66 potential mRNA targets of these microRNAs, many of which are implicated in TGFβ signaling pathway but also in pathways involving cellular metabolism and immunomodulation. A robust association exists between familial cardiovascular disease and placental microRNA expression which may be implicated in both placental insufficiencies and the developmental programming of chronic disease.

Maternal depression and adverse neighbourhood conditions during pregnancy are associated with gestational epigenetic age deceleration

Gestational epigenetic age (GEA) acceleration and deceleration can indicate developmental risk and may help elucidate how prenatal exposures lead to offspring outcomes. Depression and neighbourhood conditions during pregnancy are well-established determinants of birth and child outcomes. Emerging research suggests that maternal depression may contribute to GEA deceleration. It is unknown whether prenatal neighbourhood adversity would likewise influence GEA deceleration. This study examined whether maternal depression and neighbourhood conditions independently or jointly contributed to GEA deceleration, and which social and environmental neighbourhood conditions were associated with GEA. Participants were from the Albany Infant and Mother Study (n = 204), a prospective non-probability sampled cohort of higher risk racial/ethnic diverse mother/infant dyads. GEA was estimated from cord blood. Depressive symptoms and census-tract level neighbourhood conditions were assessed during pregnancy. Maternal depression (β = -0.03, SE = 0.01, p = 0.008) and neighbourhood adversity (β = -0.32, SE = 0.14, p = 0.02) were independently associated with GEA deceleration, controlling for all covariates including antidepressant use and cell type proportions. Neighbourhood adversity did not modify the association of maternal depression and GEA (β = 0.003, SE = 0.03, p = 0.92). igher levels of neighbourhood poverty, public assistance, and lack of healthy food access were each associated with GEA deceleration; higher elementary school test scores (an indicator of community tax base) were associated with GEA acceleration (all p < 0.001). The results of this study indicated that maternal depression and neighbourhood conditions were independently and cumulatively associated GEA in this diverse population.

Prenatal lead (Pb) exposure is associated with differential placental DNA methylation and hydroxymethylation in a human population

Prenatal lead (Pb) exposure is associated with adverse developmental outcomes and to epigenetic alterations such as DNA methylation and hydroxymethylation in animal models and in newborn blood. Given the importance of the placenta in foetal development, we sought to examine how prenatal Pb exposure was associated with differential placental DNA methylation and hydroxymethylation and to identify affected biological pathways linked to developmental outcomes. Maternal (n = 167) and infant (n = 172) toenail and placenta (n = 115) samples for prenatal Pb exposure were obtained from participants in a US birth cohort, and methylation and hydroxymethylation data were quantified using the Illumina Infinium MethylationEPIC BeadChip. An epigenome-wide association study was applied to identify differential methylation and hydroxymethylation associated with Pb exposure. Biological functions of the Pb-associated genes were determined by overrepresentation analysis through ConsensusPathDB. Prenatal Pb quantified from maternal toenail, infant toenail, and placenta was associated with 480, 27, and 2 differentially methylated sites (q < 0.05), respectively, with both increases and decreases associated with exposure. Alternatively, we identified 2, 1, and 14 differentially hydroxymethylated site(s) associated with maternal toenail, infant toenail, and placental Pb, respectively, with most showing increases in hydroxymethylation with exposure. Significantly overrepresented pathways amongst genes associated with differential methylation and hydroxymethylation (q < 0.10) included mechanisms pertaining to nervous system and organ development, calcium transport and regulation, and signalling activities. Our results suggest that both methylation and hydroxymethylation in the placenta can be variable based on Pb exposure and that the pathways impacted could affect placental function.

Selenium-associated differentially expressed microRNAs and their targeted mRNAs across the placental genome in two U.S. birth cohorts

Selenium is an important micronutrient for foetal development. MicroRNAs play an important role in the function of the placenta, in communication between the placenta and maternal systems, and their expression can be altered through environmental and nutritional cues. To investigate the associations between placental selenium concentration and microRNA expression in the placenta, our observational study included 393 mother-child pairs from the New Hampshire Birth Cohort Study (NHBCS) and the Rhode Island Child Health Study (RICHS). Placental selenium concentrations were quantified using inductively coupled plasma mass spectrometry, and microRNA transcripts were measured using RNA-seq. We fit negative binomial additive models for assessing the association between selenium and microRNAs. We used the microRNA Data Integration Portal (mirDIP) to predict the target mRNAs of the differentially expressed microRNAs and verified the relationships between miRNA and mRNA targets in a subset of samples using existing whole transcriptome data (N = 199). We identified a non-monotonic association between selenium concentration and the expression of miR-216a-5p/miR-217-5p cluster (effective degrees of freedom, EDF = 2.44 and 2.08; FDR = 3.08 × 10-5) in placenta. Thirty putative target mRNAs of miR-216a-5p and/or miR-217-5p were identified computationally and empirically and were enriched in selenium metabolic pathways (driven by selenoprotein coding genes, TXNRD2 and SELENON). Our findings suggest that selenium influences placental microRNA expression. Further, miR-216a-5p and its putative target mRNAs could be the potential mechanistic targets of the health effect of selenium.

Longitudinal changes in epigenetic age in youth with perinatally acquired HIV and youth who are perinatally HIV-exposed uninfected

OBJECTIVES

To quantify the rate of change in epigenetic age compared with chronological age over time in youth with perinatally acquired HIV (YPHIV) and youth who are perinatally HIV-exposed uninfected (YPHEU).

DESIGN

Longitudinal study of 32 YPHIV and 8 YPHEU with blood samples collected at two time points at least 3 years apart.

METHODS

DNA methylation was measured using the Illumina MethylationEPIC array and epigenetic age was calculated using the Horvath method. Linear mixed effects models were fit to estimate the average change in epigenetic age for a 1-year change in chronological age separately for YPHIV and YPHEU.

RESULTS

Median age was 10.9 and 16.8 years at time 1 and 2, respectively. Groups were balanced by sex (51% male) and race (67% black). Epigenetic age increased by 1.23 years (95% CI 1.03--1.43) for YPHIV and 0.95 years (95% CI 0.74--1.17) for YPHEU per year increase in chronological age. Among YPHIV, in a model with chronological age, a higher area under the curve (AUC) viral load was associated with an increase in epigenetic age over time [2.19 years per log10 copies/ml, (95% CI 0.65--3.74)], whereas a higher time-averaged AUC CD4+ T-cell count was associated with a decrease in epigenetic age over time [-0.34 years per 100 cells/μl, (95% CI -0.63 to -0.06)] in YPHIV.

CONCLUSION

We observed an increase in the rate of epigenetic aging over time in YPHIV, but not in YPHEU. In YPHIV, higher viral load and lower CD4+ T-cell count were associated with accelerated epigenetic aging, emphasizing the importance of early and sustained suppressive treatment for YPHIV, who will receive lifelong ART.

Extracellular vesicle microRNA in early versus late pregnancy with birth outcomes in the MADRES study

Circulating miRNA may contribute to the development of adverse birth outcomes. However, few studies have investigated extracellular vesicle (EV) miRNA, which play important roles in intercellular communication, or compared miRNA at multiple time points in pregnancy. In the current study, 800 miRNA were profiled for EVs from maternal plasma collected in early (median: 12.5 weeks) and late (median: 31.8 weeks) pregnancy from 156 participants in the MADRES Study, a health disparity pregnancy cohort. Associations between miRNA and birth weight, birth weight for gestational age (GA), and GA at birth were examined using covariate-adjusted robust linear regression. Differences by infant sex and maternal BMI were also investigated. Late pregnancy measures of 13 miRNA were associated with GA at birth (P_FDR<0.050). Negative associations were observed for eight miRNA (miR-4454+ miR-7975, miR-4516, let-7b-5p, miR-126-3p, miR-29b-3p, miR-15a-5p, miR-15b-5p, miR-19b-3p) and positive associations for five miRNA (miR-212-3p, miR-584-5p, miR-608, miR-210-3p, miR-188-5p). Predicted target genes were enriched (P_FDR<0.050) in pathways involved in organogenesis and placental development. An additional miRNA (miR-107), measured in late pregnancy, was positively associated with GA at birth in infants born to obese women (P_FDR for BMI interaction = 0.011). In primary analyses, the associations between early pregnancy miRNA and birth outcomes were not statistically significant (P_FDR≥0.05). However, sex-specific associations were observed for early pregnancy measures of 37 miRNA and GA at birth (P_FDR for interactions<0.050). None of the miRNA were associated with fetal growth measures (P_FDR≥0.050). Our findings suggest that EV miRNA in both early and late pregnancy may influence gestational duration.

Impact of comorbidities and treatment burden on general well-being among women's cancer survivors

BACKGROUND

Gains in cancer detection and treatment have meant that more patients are now living with both cancer and other chronic health conditions, which may become burdensome. We used the Patient Experience with Treatment and Self-Management (PETS) framework to study challenges in self-management and its impact on health among survivors of women's cancers who are caring for other chronic health conditions.

METHODS

Applicability of the PETS domains among survivors of women's cancers with comorbidities was assessed in focus groups to create the study survey. Women surviving primary breast, cervical, ovarian, or endometrial/uterine cancer treated between 6 months and 3 years prior at two large healthcare systems in Virginia were mailed study invitation letters to complete a telephone-based survey. The survey included questions on cancer treatment history, comorbid conditions prior to cancer, treatment and self-management experiences, health literacy, financial security, and items on self-management activities, self-management difficulties and self-management impact (i.e., role/social activity limitations and physical/mental exhaustion). Additionally, general health was assessed with items from the Patient-Reported Outcomes Measurement Information System (PROMIS). Hierarchical regression models and path analysis were used to examine correlates of self-management impact on general physical health (GPH) and mental health (GMH).

RESULTS

Of 1448 patients contacted by mail, 274 (26%) returned an interest form providing their consent to be contacted. Of these, 183 completed the survey. Reasons for non-completion included ineligibility (42), unable to be reached (33) and refusal (6). The majority were survivors of breast (58%) or endometrial/uterine cancer (28%), and 45% resided in non-urban locations. After adjusting for age, race, and cancer type, survivors with higher self-management difficulty reported higher self-management impact, which was associated with lower perceived general health. Reports of higher self-management impact was associated with being single or unmarried, white race, fulltime employed, higher financial insecurity, lower health literacy and more comorbidities. In path analysis, self-management impact was a significant mediator in the association of comorbidity and financial insecurity on GPH and GMH.

CONCLUSIONS

Among survivors of women's cancer, pre-diagnosis comorbidity, health literacy, and financial security are associated with psychosocial impact of self-management and general physical and mental health in the 6 month to 3-year period after cancer treatment has ended. The impact of self-management on psychosocial functioning is an important factor among cancer survivors caring for multiple chronic health conditions. This study provides evidence on the importance of assessing cancer survivors' self-management difficulties such as in future interventions to promote health and wellness.

Placental microRNA expression associates with birthweight through control of adipokines: results from two independent cohorts

MicroRNAs are non-coding RNAs that regulate gene expression post-transcriptionally. In the placenta, the master regulator of foetal growth and development, microRNAs shape the basic processes of trophoblast biology and specific microRNA have been associated with foetal growth. To comprehensively assess the role of microRNAs in placental function and foetal development, we have performed small RNA sequencing to profile placental microRNAs from two independent mother-infant cohorts: the Rhode Island Child Health Study (n = 225) and the New Hampshire Birth Cohort Study (n = 317). We modelled microRNA counts on infant birthweight percentile (BWP) in each cohort, while accounting for race, sex, parity, and technical factors, using negative binomial generalized linear models. We identified microRNAs that were differentially expressed (DEmiRs) with BWP at false discovery rate (FDR) less than 0.05 in both cohorts. hsa-miR-532-5p (miR-532) was positively associated with BWP in both cohorts. By integrating parallel whole transcriptome and small RNA sequencing in the RICHS cohort, we identified putative targets of miR-532. These targets are enriched for pathways involved in adipogenesis, adipocytokine signalling, energy metabolism, and hypoxia response, and included Leptin, which we further demonstrated to have a decreasing expression with increasing BWP, particularly in male infants. Overall, we have shown a robust and reproducible association of miR-532 with BWP, which could influence BWP through regulation of adipocytokines Leptin and Adiponectin.

Exposure to polybrominated biphenyl (PBB) associates with genome-wide DNA methylation differences in peripheral blood

In 1973, Michigan residents were exposed to polybrominated biphenyl (PBB) when it was accidentally added to farm animal feed. Highly exposed individuals and their children have experienced endocrine-related health problems, though the underlying mechanism behind these remains unknown. We investigated whether PBB exposure is associated with variation in DNA methylation in peripheral blood samples from 658 participants of the Michigan PBB registry using the MethylationEPIC BeadChip, as well as investigated what the potential function of the affected regions are and whether these epigenetic marks are known to associate with endocrine system pathways. After multiple test correction (FDR <0.05), 1890 CpG sites associated with total PBB levels. These CpGs were not enriched in any particular biological pathway, but were enriched in enhancer and insulator regions, and depleted in regions near the transcription start site or in CpG islands (p < 0.05). They were also more likely to be in ARNT and ESR2 transcription factor binding sites (p = 3.27e-23 and p = 1.62e-6, respectively), and there was significant overlap between CpGs associated with PBB and CpGs associated with estrogen (p < 2.2e-16). PBB-associated CpGs were also enriched for CpGs known to be associated with gene expression in blood (eQTMs) (p < 0.05). These eQTMs were enriched for pathways related to immune function and endocrine-related autoimmune disease (FDR <0.05). These results indicate that exposure to PBB is associated with differences in epigenetic marks that suggest that it is acting similarly to estrogen and is associated with dysregulated immune system pathways.

Association between one-carbon metabolism indices and DNA methylation status in maternal and cord blood

One-carbon metabolism is essential for multiple cellular processes and can be assessed by the concentration of folate metabolites in the blood. One-carbon metabolites serve as methyl donors that are required for epigenetic regulation. Deficiencies in these metabolites are associated with a variety of poor health outcomes, including adverse pregnancy complications. DNA methylation is known to vary with one-carbon metabolite concentration, and therefore may modulate the risk of adverse pregnancy outcomes. This study addresses changes in one-carbon indices over pregnancy and the relationship between maternal and child DNA methylation and metabolite concentrations by leveraging data from 24 mother-infant dyads. Five of the 13 metabolites measured from maternal blood and methylation levels of 993 CpG sites changed over the course of pregnancy. In dyads, maternal and fetal one-carbon concentrations were highly correlated, both early in pregnancy and at delivery. The 993 CpG sites whose methylation levels changed over pregnancy in maternal blood were also investigated for associations with metabolite concentrations in infant blood at delivery, where five CpG sites were associated with the concentration of at least one metabolite. Identification of CpG sites that change over pregnancy may result in better characterization of genes and pathways involved in maintaining a healthy, term pregnancy.

An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells

Background

Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome.

Results

We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60–70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control.

Conclusions

This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4842-3) contains supplementary material, which is available to authorized users.

An epigenetic clock for gestational age at birth based on blood methylation data

Background

Gestational age is often used as a proxy for developmental maturity by clinicians and researchers alike. DNA methylation has previously been shown to be associated with age and has been used to accurately estimate chronological age in children and adults. In the current study, we examine whether DNA methylation in cord blood can be used to estimate gestational age at birth.

Results

We find that gestational age can be accurately estimated from DNA methylation of neonatal cord blood and blood spot samples. We calculate a DNA methylation gestational age using 148 CpG sites selected through elastic net regression in six training datasets. We evaluate predictive accuracy in nine testing datasets and find that the accuracy of the DNA methylation gestational age is consistent with that of gestational age estimates based on established methods, such as ultrasound. We also find that an increased DNA methylation gestational age relative to clinical gestational age is associated with birthweight independent of gestational age, sex, and ancestry.

Conclusions

DNA methylation can be used to accurately estimate gestational age at or near birth and may provide additional information relevant to developmental stage. Further studies of this predictor are warranted to determine its utility in clinical settings and for research purposes. When clinical estimates are available this measure may increase accuracy in the testing of hypotheses related to developmental age and other early life circumstances.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1068-z) contains supplementary material, which is available to authorized users.

The transcriptional landscape of age in human peripheral blood

Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.

Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.

Miocene Fossils Reveal Ancient Roots for New Zealand's Endemic Mystacina (Chiroptera) and Its Rainforest Habitat

The New Zealand endemic bat family Mystacinidae comprises just two Recent species referred to a single genus, Mystacina. The family was once more diverse and widespread, with an additional six extinct taxa recorded from Australia and New Zealand. Here, a new mystacinid is described from the early Miocene (19-16 Ma) St Bathans Fauna of Central Otago, South Island, New Zealand. It is the first pre-Pleistocene record of the modern genus and it extends the evolutionary history of Mystacina back at least 16 million years. Extant Mystacina species occupy old-growth rainforest and are semi-terrestrial with an exceptionally broad omnivorous diet. The majority of the plants inhabited, pollinated, dispersed or eaten by modern Mystacina were well-established in southern New Zealand in the early Miocene, based on the fossil record from sites at or near where the bat fossils are found. Similarly, many of the arthropod prey of living Mystacina are recorded as fossils in the same area. Although none of the Miocene plant and arthropod species is extant, most are closely related to modern taxa, demonstrating potentially long-standing ecological associations with Mystacina.

A survey of management practices on Irish dairy farms with emphasis on risk factors for Johne's disease transmission

BACKGROUND

Johne's disease (JD) is a chronic granulomatous enteritis affecting ruminants. A number of farm management practices are associated with increased risk of JD transmission. The aim of the current study was to document JD-related management practices currently employed on Irish dairy farms. Survey questions focused on calving area (CA), calf and manure management. Independent variables (region, calving-season, enterprise type, herd size and biosecurity status) were used to examine influences on JD associated dependent variables (survey questions). Additionally general biosecurity practices were also examined.

RESULTS

Results showed management practices implemented by Irish dairy farmers pose a high risk of JD transmission. Of the farmers surveyed, 97% used the CA for more than one calving, 73.5% and 87.8% pooled colostrum and milk respectively, 33.7% never cleaned the CA between calving's, and 56.6% used the CA for isolating sick cows. Survey results also highlighted that larger herds were more likely to engage in high risk practices for JD transmission, such as pooling colostrum (OR 4.8) and overcrowding the CA (OR 7.8). Larger herds were also less likely than smaller herds to clean the CA (OR 0.28), a practice also considered of risk in the transmission of JD.

CONCLUSION

Many management practices associated with risk of JD transmission were commonly applied on Irish dairy farms. Larger herds were more likely to engage in high risk practices for JD transmission. Control programmes should incorporate educational tools outlining the pathogenesis and transmission of JD to highlight the risks associated with implementing certain management practices with regard to JD transmission.

A filter-based propidium monoazide technique to distinguish live from membrane-compromised microorganisms using quantitative PCR

Propidium monoazide (PMA) was used to differentiate live from membrane-compromised bacteria in PCR methods. We have adapted this technique for use on membrane-filtered water samples and determined its efficacy using qPCR. Independent labs at three institutions replicated these findings.

Assessing influence of experimental parameters on formation of PCDD/F from ash derived from fires of CCA-treated wood

Ash residues from fires of radiata pine timber, both untreated and treated with chromated copper arsenate (CCA), were analyzed for the presence of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/F). Fire conditions were simulated using a cone calorimeter. The sensitivity of the magnitude and profile of PCDD/F in the ash under controlled experimental conditions were examined to gain an insight into the formation of PCDD/F in a system containing CCA. The total amount of PCDD/F increased from 2.0 ng/kg of ash (0.05 ng of TE/kg of ash, using WHO-TEF) for untreated radiata pine to a maximum of 2700 ng/kg of ash (78 ng of TE/kg of ash) for 0.94% CCA. Ash containing CCA showed a distinct preference for formation of PCDFs, particularly the tetrachloro homologue. It is concluded that PCDD/F formation predominantly occurred via de novo synthesis during smoldering of the char rather than during the initial flaming and pyrolysis. Furthermore, the composition of the CCA constituents present in the timber was controlled to assess whether the physical presence of Cu, a known catalyst in PCDD/F production, was sufficient to account for the formation of PCDD/F in fires of timber impregnated with CCA.

Increased PCDD/F formation in the bottom ash from fires of CCA-treated wood

Bottom ash that was the result of the combustion of chromated copper arsenate (CCA) treated wood under controlled fire conditions showed an increase of several orders of magnitude in the levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), compared to that of untreated timber. Wood that has been pressure treated with CCA contains copper (II), which is known to catalyse the so-called de novo formation of PCDD/Fs. Comparable levels of PCDD/Fs would be expected in residual ash from burning CCA-treated wood in backyard fires, stoves and wood heaters, as a consequence of similar combustion conditions.

Making mistakes in practice. Developing a consensus statement

OBJECTIVE

To develop a reference statement for the appropriate management of mistakes in the general practice training environment.

METHOD

The setting was a series of focus groups held during workshops with The Royal Australian College of General Practitioners Training Program in the Northern Territory (NT). The participants included NT supervisors and registrars, and representatives of the Consumer Reference Group, Top End Division of General Practice.

RESULTS

A reference statement and mutually agreed list of duties for registrars, their supervisors and patients.

CONCLUSION

Mistakes are a part of the practice of medicine and can impact on everyone. An appropriate response and the opportunity to reflect and learn from the experience are important elements in minimising the adverse impact. We recommend that the issue of mistakes be considered a priority in the teaching of medicine.

The JIM interview. Edward M. Kennedy, United States Senator

Senator Edward M. Kennedy has represented Massachusetts in the United States Senate for thirty-six years. He was first elected in 1962 to finish the term of his brother, President John F. Kennedy. Since then, he has been elected to six full terms, and he is now the third most senior member of the senate. The efforts to bring quality health care to every American is a battle that Kennedy has been waging ever since he arrived in the Senate. Recent achievements include the Health Insurance Portability and Accountability Act of 1996, which makes it easier for those who change their job or lose their job to keep their health insurance, and the Children's Health Insurance Act of 1997, which makes health insurance more widely available to children through age 18 in all 50 states. A strong supporter of clinical research, Senator Kennedy cosponsored the Clinical Research Enhancement Act and has been a vocal advocate of stem cell research. He is currently the senior Democrat on the Labor and Human Resources committee in the Senate.

Home care and the ADA: do limitations on coverage violate the law?

To avoid liability, home care agencies must have a firm grasp of the basic requirements of the Americans with Disabilities Act (ADA) and Section 504 of the Rehabilitation Act of 1973 ("Section 504"). Agency leaders must understand the legal issues that arise whenever care is limited or denied to persons with disabilities.

Transpalatal approach for the extracranial surgical repair of transsphenoidal cephaloceles in children

The surgical treatment of transsphenoidal cephaloceles in children is controversial. Reduction and repair via a transcranial approach are associated with high postoperative rates of morbidity, mortality, and hypothalamic dysfunction. In this study, four patients, aged 3 to 35 months at surgery, underwent successful transpalatal repair of two encephaloceles and two meningoceles. Two patients presented with nasal obstruction in infancy, one presented with unexplained meningitis, and in one patient the lesion was found incidentally during evaluation for seizures. Two children had median cleft face syndrome, another had an associated Arnold-Chiari type I malformation, and the fourth had no other cranial abnormalities. All patients underwent preoperative evaluation including magnetic resonance (MR) imaging. Auditory, ophthalmological, genetic, endocrinological, or other evaluation was undertaken as indicated. Lesions were approached through the median raphe of the hard and soft palates. All cephaloceles were easily visualized and dissected after division of the nasal palatal mucosa. The dural sac and its contents were reduced by surface coagulation after division and dissection of the overlying mucosa. Once reduced, the bone defect was obliterated in three of four patients. The dura was not opened and anomalous neural elements were not resected. At follow-up evaluation, all patients demonstrated resolution of preoperative symptoms without evidence of infection or lasting morbidity. Follow-up MR imaging showed reduction in all cases. The authors conclude that this transpalatal approach is safe and reliable for the treatment of transsphenoidal cephaloceles in young children.

Absence of maladaptive neuronal plasticity after genitofemoral-ilioinguinal neurectomy

BACKGROUND

Pain (neuralgia) and paresthesia in the inguinal region after lower abdominal surgery is rare. Historically, treatment consisted of neurolysis, local injections, and administration of various medications. The management of chronic pain syndromes is often coordinated by anesthesiologists. Neurolytic therapy is seldom recommended, on the basis of the theory of maladaptive neuronal plasticity.

METHODS

Twenty-three patients underwent genitofemoral neurectomy at our institution between 1981 and 1990. Records were reviewed to determine preoperative symptoms, evaluation, and treatment. Patients were contacted and questioned about current symptoms and disability.

RESULTS

All records were reviewed. Sixteen (70%) of the patients were located for long-term follow-up. Patients were symptomatic for an average of 3.3 years and underwent 3.1 operations before referral. Inguinal herniorrhaphy was the most common initial surgery (14 of 16 patients). All patients underwent multidisciplinary evaluation. Fifteen underwent L1-2 paraspinous nerve block, and 13 had total pain relief. Postoperative follow-up ranged from 36 to 144 months. Ten patients reported significant pain relief, and three patients reported slight improvement. Three of the six patients who had persistent neuralgia had significant orchialgia. None of the patients who had significant relief had preoperative testicular pain.

CONCLUSIONS

Genitofemoral neurectomy provided long-term relief in 62.5% of patients with genitofemoral neuralgia. Severe testicular pain indicated a less favorable outcome. These data do not support the maladaptive neuronal plasticity theory but do support early referral of some patients for neurectomy.

Finding a lasting cure for U.S. health care

In "Making Competition in Health Care Work" (July-August 1994), Elizabeth Olmsted Teisberg, Michael E. Porter, and Gregory B. Brown ask a question that has been absent from the national debate on health care reform: How can the United States achieve sustained cost reductions while at the same time maintaining quality of care? The authors argue that innovation driven by rigorous competition is the key to successful reform. A lasting cure for health care in the United States should include four basic elements: corrected incentives to spur productive competition, universal insurance to secure economic efficiency, relevant information to ensure meaningful choice, and innovation to guarantee dynamic improvement. In this issue's Perspectives section, eleven experts examine the current state of the health care system and offer their views on the shape that reform should take. Some excerpts: "On the road to innovation, let us not forget to develop the tools that allow physicians, payers, and patients to make better decisions." I. Steven Udvarhelyi; "Health care is not a product or service that can be standardized, packaged, marketed, or adequately judged by consumers according to quality and price." Arnold S. Relman; "Just as antitrust laws are the wise restraints that make competition free in other sectors of the economy, so the right kind of managed competition can work well in health care." Edward M. Kennedy "Biomedical research should be considered primarily an investment in the national economic well-being with additional humanitarian benefits." Elizabeth Marincola.

Primary nonfunction. Is there a contribution from the back table bath?

A persistent problem in orthotopic liver transplantation (OLT) is primary nonfunction (PNF) of the hepatic allograft. In most instances the cause of the failure is unknown. In an attempt to minimize these graft failure, modifications in the procurement and operative procedure have been investigated. One change in the procedure at the University of Nebraska Medical Center has been the monitoring of the temperature of the fluid in the back table bath during preparation of the donor liver. Our initial procedure involved creating an ice slurry of lactated Ringer's solution and ice slush in which the donor liver was then prepared. The temperature of this ice slurry was retrospectively found to be from -3 degrees C to -1 degrees C (group I). In this group there was a higher-than-expected incidence of PNF. To investigate whether the temperature of the back table bath influenced the incidence of PNF, beginning with transplant No. 42 the preparation of the back table bath was modified. The bath was created by adding a small amount of PlasmaLyte slush to 2 L of PlasmaLyte (group II). The temperature of the bath was maintained at 2-4 degrees C. Data were collected on 100 consecutive liver transplants. All transplants were performed using standard techniques, the operation for the two groups differing only as described above. Transaminase levels were followed as an index of the allograft function and were expected to begin to normalize within 2-3 days after transplantation. While both groups display this trend, transaminase levels in group II were significantly lower postoperatively than group I levels (P less than 0.05). Preoperative values were similar. There were 7 PNFs in group I; 0 in group II (P less than 0.005). We feel that the change in the back table procedure has positively influenced the function of the hepatic allografts, and we conclude that transplant centers need to monitor the temperature at which all allografts are stored and prepared, and the cognizant that this may influence the postoperative function of the transplanted liver.

Clinical patterns of cytomegalovirus disease after liver transplantation

During a 43-month period, we performed 248 liver transplantations in 211 patients (127 adults and 84 children). Cytomegalovirus (CMV) disease was documented in 73 recipients (34.6%). Risk factors for CMV disease included donor CMV seropositivity, antilymphocyte therapy, and retransplantation. The mean time of occurrence of CMV disease was 38.3 days after transplantation, and the most frequent site of disease was the hepatic allograft. A total of 69 patients were treated with intravenous ganciclovir, with a prompt and lasting response documented in 51 (73.9%). The remaining 18 (26.1%) developed recurrent CMV disease, which was more common after primary CMV exposure. Cytomegalovirus disease was ultimately controlled by ganciclovir in 94.2% of cases. This disease occurs early after transplantation and can be related to well-defined risk factors. Although ganciclovir therapy is effective, preliminary experience with prophylaxis shows promise in reducing the incidence of CMV disease.

Fentanyl intermittent bolus technique for anesthesia in infants and children undergoing cardiac surgery

The use of fentanyl by an incremental intravenous (IV) bolus technique was evaluated in eight pediatric patients (ages 4 months to 5 years, ASA III-IV) undergoing corrective surgery for congenital heart defects. Anesthesia was induced with 5 to 10 micrograms/kg of fentanyl. Additional boluses of comparable size were given intermittently thereafter, in order that a total dose of 100 micrograms/kg was achieved just before instituting cardiopulmonary bypass (CPB). Heart rate, systolic blood pressure, various measures of anesthetic depth, and plasma fentanyl levels measured by radioimmunoassay were compared at various points during anesthesia, surgery, and recovery. Decreases in heart rate were observed at the time of sternal incision and at 30 minutes thereafter, when doses of fentanyl were near-maximal. No changes from baseline in systolic blood pressure or in anesthetic depth occurred at any of the intervals studied. The plasma concentration of fentanyl was 30 +/- 8 ng/mL just after completion of the fentanyl administration, immediately before CPB. With onset of CPB, the fentanyl level fell to 13 +/- 9 ng/mL, a statistically significant difference from the baseline value. No further change occurred over the additional 231 +/- 74 minutes in the operating room. The fentanyl concentration was 10 +/- 4 ng/mL upon entry into the recovery room. It is concluded that administration of fentanyl in small, intermittent IV boluses, with dosing completed before the onset of CPB, produces satisfactory plasma levels, anesthesia, and hemodynamic stability in children undergoing corrective surgery for congenital cardiac defects.

Serum concentrations of prostacyclin and thromboxane in children before, during, and after cardiopulmonary bypass

Twenty-six consecutive pediatric patients undergoing reparative procedures necessitating cardiopulmonary bypass were prospectively studied to determine changes in serum levels of 6-keto-prostaglandin F1 alpha and thromboxane B2. Cardiac lesions included acyanotic lesions (five patients), obstructive lesions (10 patients), and right-to-left shunts (11 patients). There was a significant (p less than 0.05) increase in 6-keto-prostaglandin F1 alpha from preoperative levels measured at the time of arterial and venous cannula insertion. This concentration was maintained throughout cardiopulmonary bypass and remained significantly elevated (p less than 0.001) in the recovery room, but returned to preoperative levels by the morning after the operation. Preoperative levels of thromboxane B2 varied widely and were not significantly different from intraoperative levels. The postoperative levels of thromboxane B2, however, were significantly different (p less than 0.05) from the intraoperative levels. In the pediatric age group undergoing cardiopulmonary bypass, 6-keto-prostaglandin F1 alpha and thromboxane B2 change during bypass but do not significantly differ when preoperative levels are compared to postoperative values.