Arsenic exposure and human blood DNA methylation and hydroxymethylation profiles in two diverse populations from Bangladesh and Spain.

BACKGROUND: Associations of arsenic (As) with the sum of 5-mC and 5-hmC levels have been reported; however, As exposure-related differences of the separated 5-mC and 5-hmC markers have rarely been studied. METHODS: In this study, we evaluated the association of arsenic exposure biomarkers and 5-mC and 5-hmC in 30 healthy men (43-55 years) from the Aragon Workers Health Study (AWHS) (Spain) and 31 healthy men (31-50 years) from the Folic Acid and Creatinine Trial (FACT) (Bangladesh). We conducted 5-mC and 5-hmC profiling using Infinium MethylationEPIC arrays, on paired standard and modified (ox-BS in AWHS and TAB in FACT) bisulfite converted blood DNA samples. RESULTS: The median for the sum of urine inorganic and methylated As species (ΣAs) (µg/L) was 12.5 for AWHS and 89.6 for FACT. The median of blood As (µg/L) was 8.8 for AWHS and 10.2 for FACT. At a statistical significance p-value cut-off of 0.01, the differentially methylated (DMP) and hydroxymethylated (DHP) positions were mostly located in different genomic sites. Several DMPs and DHPs were consistently found in AWHS and FACT both for urine ΣAs and blood models, being of special interest those attributed to the DIP2C gene. Three DMPs (annotated to CLEC12A) for AWHS and one DHP (annotated to NPLOC4) for FACT remained statistically significant after false discovery rate (FDR) correction. Pathways related to chronic diseases including cardiovascular, cancer and neurological were enriched. CONCLUSIONS: While we identified common 5-hmC and 5-mC signatures in two populations exposed to varying levels of inorganic As, differences in As-related epigenetic sites across the study populations may additionally reflect low and high As-specific associations. This work contributes a deeper understanding of potential epigenetic dysregulations of As. However, further research is needed to confirm biological consequences associated with DIP2C epigenetic regulation and to investigate the role of 5-hmC and 5-mC separately in As-induced health disorders at different exposure levels.

MLML2R: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions.

Accurately measuring epigenetic marks such as 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level, requires combining data from DNA processing methods including traditional (BS), oxidative (oxBS) or Tet-Assisted (TAB) bisulfite conversion. We introduce the R package MLML2R, which provides maximum likelihood estimates (MLE) of 5-mC and 5-hmC proportions. While all other available R packages provide 5-mC and 5-hmC MLEs only for the oxBS+BS combination, MLML2R also provides MLE for TAB combinations. For combinations of any two of the methods, we derived the pool-adjacent-violators algorithm (PAVA) exact constrained MLE in analytical form. For the three methods combination, we implemented both the iterative method by Qu et al. [Qu, J., M. Zhou, Q. Song, E. E. Hong and A. D. Smith (2013): "Mlml: consistent simultaneous estimates of dna methylation and hydroxymethylation," Bioinformatics, 29, 2645-2646.], and also a novel non iterative approximation using Lagrange multipliers. The newly proposed non iterative solutions greatly decrease computational time, common bottlenecks when processing high-throughput data. The MLML2R package is flexible as it takes as input both, preprocessed intensities from Infinium Methylation arrays and counts from Next Generation Sequencing technologies. The MLML2R package is freely available at https://CRAN.R-project.org/package=MLML2R.

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.

First identified as histone-modifying proteins, lysine acetyltransferases (KATs) and deacetylases (KDACs) antagonize each other through modification of the side chains of lysine residues in histone proteins. Acetylation of many non-histone proteins involved in chromatin, metabolism or cytoskeleton regulation were further identified in eukaryotic organisms, but the corresponding enzymes and substrate-specific functions of the modifications are unclear. Moreover, mechanisms underlying functional specificity of individual KDACs remain enigmatic, and the substrate spectra of each KDAC lack comprehensive definition. Here we dissect the functional specificity of 12 critical human KDACs using a genome-wide synthetic lethality screen in cultured human cells. The genetic interaction profiles revealed enzyme-substrate relationships between individual KDACs and many important substrates governing a wide array of biological processes including metabolism, development and cell cycle progression. We further confirmed that acetylation and deacetylation of the catalytic subunit of the adenosine monophosphate-activated protein kinase (AMPK), a critical cellular energy-sensing protein kinase complex, is controlled by the opposing catalytic activities of HDAC1 and p300. Deacetylation of AMPK enhances physical interaction with the upstream kinase LKB1, leading to AMPK phosphorylation and activation, and resulting in lipid breakdown in human liver cells. These findings provide new insights into previously underappreciated metabolic regulatory roles of HDAC1 in coordinating nutrient availability and cellular responses upstream of AMPK, and demonstrate the importance of high-throughput genetic interaction profiling to elucidate functional specificity and critical substrates of individual human KDACs potentially valuable for therapeutic applications.

Organismal Responses to Hypoxemic Challenges.

As a counterpoint to the volumes of beautiful work exploring how the carotid bodies (CBs) sense and transduce stimuli into neural traffic, this study explored one organismal reflex response to such stimulation. We challenged the anesthetized, paralyzed, artificially ventilated cat with two forms of acute hypoxemia: 10 % O(2)/balance N(2) (hypoxic hypoxia [HH] and carbon monoxide hypoxia [COH]). HH stimulates both CBs and aortic bodies (ABs), whereas COH stimulates only the ABs. Our design was to stimulate both with HH (HHint), then to stimulate only the ABs with COH (COHint); then, after aortic depressor nerve transaction, only the CBs with HH (HHabr), and finally neither with COH (COHabr). We recorded whole animal responses from Group 1 cats (e.g., cardiac output, arterial blood pressure, pulmonary arterial pressure/and vascular resistance) before and after sectioning the aortic depressor nerves. From Group 2 cats (intact) and Group 3 cats (aortic body resected) we recorded the vascular resistance in several organs (e.g., brain, heart, spleen, stomach, pancreas, adrenal glands, eyes). The HHint challenge was the most effective at keeping perfusion pressures adequate to maintain homeostasis in the face of a systemic wide hypoxemia with locally mediated vasodilation. The spleen and pancreas, however, showed a vasoconstrictive response. The adrenals and eyes showed a CB-mediated vasodilation. The ABs appeared to have a significant impact on the pulmonary vasculature as well as the stomach. Chemoreceptors via the sympathetic nervous system play the major role in this organism's response to hypoxemia.

A multiparametric and orthogonal approach indicates low toxicity for zein nanoparticles in a repellent formulation.

The incidence of viruses such as Zika, Dengue, and Chikungunya affects human health worldwide, and insect repellents are recommended for individual protection. Formulations incorporating nanotechnology should be carefully assessed for toxicity, particularly regarding the security levels established for human health and the environment. This study evaluates the cytotoxicity of a repellent formulation containing zein nanoparticles (NP) loading geraniol (Ger) and icaridin (Ica) in three cell lines: NIH/3T3, HaCaT, and SIRC. To address formulation hazards, IC50 values were determined by MTT and Calcein-AM assays. In both NIH/3T3 and HaCaT, the IC50 values for NP + Ger + Ica formulation were around 0.2%. For risk assessment, cell viability was also determined after a single exposure and repeated exposure to the formulation. No evidence of cytotoxicity was observed for NP + Ger + Ica formulation-treated cells. The risk assessment for eye damage revealed cytotoxicity in SIRC cells when exposed to a 5% concentration, which may be attributed to ocular geraniol toxicity, because zein nanoparticles alone did not exhibit any signs of toxicity. Cell internalization indicated low uptake in NIH/3T3 and HaCaT cells. Phenotypic profiling resulted in similar phenotypes for untreated cells and cells exposed to NP + Ger + Ica formulation. The toxicological profile outlined by the multiparametric and orthogonal approach suggests that the NP + Ger + Ica formulation poses no significant risk to the topical application under the tested conditions. Adopting an orthogonal approach brings robustness to our findings.

Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions.

Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. In this chapter, we illustrate how the reader can make small adjustments to these protocols to obtain estimates of methylation and hydroxymethylation proportions.

Asymptotic behavior of the scaled mutation rate estimators.

Important aspects of population evolution have been investigated using nucleotide sequences. Under the neutral Wright-Fisher model, the scaled mutation rate represents twice the average number of new mutations per generations and it is one of the key parameters in population genetics. In this study, we present various methods of estimation of this parameter, analytical studies of their asymptotic behavior as well as comparisons of the distribution's behavior of these estimators through simulations. As knowledge of the genealogy is needed to estimate the maximum likelihood estimator (MLE), an application with real data is also presented, using jackknife to correct the bias of the MLE, which can be generated by the estimation of the tree. We proved analytically that the Waterson's estimator and the MLE are asymptotically equivalent with the same rate of convergence to normality. Furthermore, we showed that the MLE has a better rate of convergence than Waterson's estimator for values of the parameter greater than one and this relationship is reversed when the parameter is less than one.

Correlation between Mitochondrial Reactive Oxygen and Severity of Atherosclerosis.

Atherosclerosis has been associated with mitochondria dysfunction and damage. Our group demonstrated previously that hypercholesterolemic mice present increased mitochondrial reactive oxygen (mtROS) generation in several tissues and low NADPH/NADP+ ratio. Here, we investigated whether spontaneous atherosclerosis in these mice could be modulated by treatments that replenish or spare mitochondrial NADPH, named citrate supplementation, cholesterol synthesis inhibition, or both treatments simultaneously. Robust statistical analyses in pooled group data were performed in order to explain the variation of atherosclerosis lesion areas as related to the classic atherosclerosis risk factors such as plasma lipids, obesity, and oxidative stress, including liver mtROS. Using three distinct statistical tools (univariate correlation, adjusted correlation, and multiple regression) with increasing levels of stringency, we identified a novel significant association and a model that reliably predicts the extent of atherosclerosis due to variations in mtROS. Thus, results show that atherosclerosis lesion area is positively and independently correlated with liver mtROS production rates. Based on these findings, we propose that modulation of mitochondrial redox state influences the atherosclerosis extent.

Autonomic regulation of organ vascular resistances during hypoxemia in the cat.

This study aimed to dissect the roles played by the autonomic interoreceptors, the carotid bodies (cbs) and the aortic bodies (abs) on the vascular resistances of several organs in anesthetized, paralyzed, artificially ventilated cats challenged by systemic hypoxemia. Two 15 min challenges stimulated each of 5 animals in two different groups: (1) in the intact group hypoxic hypoxia (10% O2 in N2; HH) stimulated both abs and cbs, increasing neural output to the nucleus tractus solitarius (NTS); (2) in this group carbon monoxide hypoxia (30% O2 in N2 with the addition of CO; COH) stimulated only the abs, increasing neural output to the NTS. (3) In the second group in which their bilateral aortic depressor nerves had been transected only the cbs increased neural output to the NTS during the HH challenge; (4) in this aortic body resected group during COH neither abs nor cbs increased neural traffic to the NTS. CO and 10% O2 reduced Hb saturation to the same level. With the use of radiolabeled microspheres blood flow was measured in a variety of organs. Organ vascular resistance was calculated by dividing the aortic pressure by that organ's blood flow. The spleen and pancreas revealed a vasoconstriction in the face of systemic hypoxemia, thought to be sympathetic nervous system (SNS)-mediated. The adrenals and the eyes vasodilated only when cbs were stimulated. Vasodilation in the heart and diaphragm showed no effect of chemoreceptor stimulated increase in SNS output. Different chemoreceptor involvement had different effects on the organs.

Autonomic control of the cardiovascular system in the cat during hypoxemia.

This study aimed to determine the roles played by the autonomic interoreceptors, the carotid bodies (cbs) and the aortic bodies (abs) in anesthetized, paralyzed, artificially ventilated cats' response to systemic hypoxemia. Four 15min challenges stimulated each of 15 animals: (1) hypoxic hypoxia (10%O2 in N2; HH) in the intact (int) cat where both abs and cbs sent neural traffic to the nucleus tractus solitarius (NTS); (2) carbon monoxide hypoxia (30%O2 in N2 with the addition of CO; COH) in the intact cat where only the abs sent neural traffic to the NTS; (3) HH in the cat after transection of both aortic depressor nerves, resecting the aortic bodies (HHabr), where only the cbs sent neural traffic to the NTS; (4) COH to the abr cat where neither abs nor cbs sent neural traffic to the NTS. Cardiac output (C.O.), contractility (dP/dt(MAX)), systolic/diastolic pressures, aortic blood pressure, total peripheral resistance, pulmonary arterial pressure, and pulmonary vascular resistance (PVR) were measured. When both cbs and abs were active the maximum increases were observed except for PVR which decreased. Some variables showed the cbs to have a greater effect than the abs. The abs proved to be important during some challenges for maintaining blood pressure. The data support the critically important role for the chemoreceptor-sympathetic nervous system connection during hypoxemia for maintaining viable homeostasis, with some differences between the cbs and the abs.

Impact of water-vending kiosks and hygiene education on household drinking water quality in rural Ghana.

Innovative solutions are essential to improving global access to potable water for nearly 1 billion people. This study presents an independent investigation of one alternative by examining for-profit water-vending kiosks, WaterHealth Centers (WHCs), in rural Ghana to determine their association with household drinking water quality. WHCs' design includes surface water treatment using filtration and ultraviolet light disinfection along with community-based hygiene education. Analyses of water samples for Escherichia coli and household surveys from 49 households across five villages collected one time per year for 3 years indicate that households using WHCs had improved water quality compared with households using untreated surface water (adjusted incidence rate ratio = 0.07, 95% confidence interval = 0.02, 0.21). However, only 38% of households used WHCs by the third year, and 60% of those households had E. coli in their water. Recontamination during water transport and storage is an obstacle to maintaining WHC-vended water quality.

Social support of low-income Brazilian mothers related to time to completion of childhood vaccinations.

Our study objective was to examine how maternal social support and depressive symptoms are associated with time to completion of childhood vaccinations. We used cross-sectional data from 582 randomly-selected, low-income Brazilian children. Adjusted Cox Proportional Hazard models were used to estimate time to completing the first three recommended oral polio and diphtheria, pertussis and tetanus (DPT) vaccinations as well as their booster doses. Among only the women with low social support, each ten-point increase on the Medical Outcomes Study - Social Support Scale was associated with a 20% increased chance of completing the first three recommended vaccinations for polio and DPT at any given time (HR = 1.20, 95% CI 1.02-1.42). Although falling short of statistical significance, also among mothers with low social support, we found a suggestive finding of increased social support associated with 25% greater chance of completing polio and DPT booster vaccines at any given time (HR = 1.25, 95% CI 0.98-1.60). There was no association between maternal depressive symptoms and vaccination completion. Among mothers with little social support, increased social support may be important for timely completion of vaccinations in low-income Brazilian children. Longitudinal studies and research on mechanisms explaining associations between maternal social support and childhood vaccination are needed.

Maternal antibody reactivity to lymphocytes of offspring with autism.

The study examined whether maternal serum antibodies from mothers of autistic children preferentially bind to lymphocytes of their autistic children compared with unaffected siblings. In a previous study, maternal serum antibodies from mothers mediated cytotoxicity with complement to lymphocytes of their autistic children. Here, maternal serum antibody binding was examined by flow cytometry. We compared levels of mothers' serum binding against peripheral blood monocytes of their autistic children vs unaffected siblings. Because the level of binding to peripheral blood monocytes could be low, binding was examined in specific lymphocyte subpopulations. In 19 samples, the mean level of maternal serum immunoglobulin G binding to CD4 and CD8 T cells, B cells, natural killer cells, and macrophages was not significantly different from the mean level of binding to unaffected siblings. The percentages of different subpopulations were not significantly different between autistic children and unaffected siblings, although a trend (P < 0.1) emerged, i.e., autistic children displayed a higher percentage of natural killer cells and a lower percentage of B cells. These findings cast doubt on a direct effect of maternal antibodies, but do not preclude potential intrauterine pathogenic immune mechanisms in autism.

The impact of hydrogen sulfide (H2S) on neurotransmitter release from the cat carotid body.

Do cat carotid bodies (CBs) increase their release of acetylcholine and ATP in response to H(2)S? Two CBs, incubated in a Krebs Ringer bicarbonate solution at 37 ° C, exhibited a normal response to hypoxia-increased release of acetylcholine (ACh) and ATP. They were challenged with several concentrations of Na(2)S, an H(2)S donor. H(2)S, a new gasotransmitter, is reported to open K(ATP) channels. Under normoxic conditions the CBs reduced their release of ACh and ATP below control values. They responded identically to pinacidil, a well-known K(ATP) channel opener. CB glomus cells exhibited a positive immunohistochemical signal for cystathione-ß-synthetase, a H(2)S synthesizing enzyme, and for a subunit of the K(ATP) channel. The data suggest that Na(2)S may have opened the glomus cells' K(ATP) channels, hyperpolarizing the cells, thus reducing their tonic release of ACh and ATP. Since during hypoxia H(2)S levels rise, the glomus cells responding very actively to hypoxia may be protected from over-exertion by the H(2)S opening of the K(ATP) channels.

Manganese exposure induces microglia activation and dystrophy in the substantia nigra of non-human primates.

Chronic manganese (Mn) exposure produces neurological deficits including a form of parkinsonism that is different from Parkinson's disease (PD). In chronic Mn exposure, dopamine neurons in the substantia nigra (SN) do not degenerate but they appear to be dysfunctional. Further, previous studies have suggested that the substantia nigra pars reticulata (SNr) is affected by Mn. In the present study, we investigated whether chronic Mn exposure induces microglia activation in the substantia nigra pars compacta (SNc) and SNr in Cynomolgus macaques. Animals were exposed to different weekly doses of Mn (3.3-5.0, 5.0-6.7, 8.3-10 mg Mn/kg body weight) and microglia were examined in the substantia nigra using LN3 immunohistochemistry. We observed that in control animals, LN3 labeled microglia were characterized by a resting phenotype. However, in Mn-treated animals, microglia increased in number and displayed reactive changes with increasing Mn exposure. This effect was more prominent in the SNr than in the SNc. In the SNr of animals administered the highest Mn dose, microglia activation was the most advanced and included dystrophic changes. Reactive microglia expressed increased iNOS, L-ferritin, and intracellular ferric iron which were particularly prominent in dystrophic compartments. Our observations indicate that moderate Mn exposure produces structural changes on microglia, which may have significant consequences on their function.