CpG islands of the vitamin D receptor gene : differential methylation and tuberculosis predisposition

M.Sc.Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). TB is a multifactorial disease, influenced by both environmental and genetic factors. Susceptibility varies among individuals and is likely explained by differential environmental exposures and genetic factors. For example, Africans are more susceptible to TB than non-Africans, likely attributed to their generally lower socioeconomic status and possible higher frequencies of ‘susceptible’ genetic variants. Similarly, males are more susceptible to TB than females, presumably as a consequence of gender-based sociocultural differences as well as biological and/or genetic differences. From a host genetic perspective, TB is a complex disease associated with variants from several genes. The Vitamin D Receptor (VDR) gene, coding for the VDR protein, has received much attention as a candidate gene; the VDR mediates vitamin D functions, of which one is to restrict M. tuberculosis survival in macrophages. Several studies attempting to associate VDR single nucleotide polymorphisms (SNPs) with TB susceptibility have given inconsistent results. Factors suggested to contribute to these inconsistencies include confounding environmental factors as well as higher VDR genetic/haplotypic diversity and less linkage disequilibrium (LD) in African populations compared to non-African populations. However, epigenetic variation has not yet been considered as an additional confounding factor leading to inconsistencies in genetic association studies for TB and VDR. vi Epigenetic factors are heritable and pivotal to regulate gene transcription. Moreover, epigenetic factors are highly susceptible to environmental influences and have been shown to be the underlying factor in certain disease aetiologies. Not only are epigenetic factors susceptible to environmental influences, but also to genetic factors acting in cis or in trans. An example is the formation or elimination of a methylatable CpG by a SNP. On the other hand, epigenetic factors may influence the genotype through formation of methylation-induced SNPs. The synergistic effect of genetic variants, epigenetic variants and the environment on disease is known as the common disease genetic epigenetic (CDGE) hypothesis. The CDGE hypothesis supports the study of both genetic and epigenetic variants to provide a better understanding of disease aetiologies and to increase the power of association studies

Systematic Review of Screening and Surveillance Programs to Protect Workers from Nanomaterials

<div><p>Background</p><p>Screening and surveillance approaches for workers exposed to nanomaterials could aid in early detection of health effects, provide data for epidemiological studies and inform action to decrease exposure. The aim of this review is to identify such screening and surveillance approaches, in order to extract available data regarding (i) the studies that have successfully been implemented in present day, (ii) identification of the most common and/or toxic nano-related health hazards for workers and (iii) possible exposure surveillance markers. This review contributes to the current understanding of the risk associated with nanomaterials by determining the knowledge gap and making recommendations based on current findings.</p><p>Methods</p><p>A systematic review was conducted. PubMed and Embase were searched to identify articles reporting on any surveillance-related study that described both exposure to nanomaterials and the health indicators that were measured. Four reviewers worked in pairs to independently assess the eligibility of studies and risk of bias before extraction of data. Studies were categorised according to the type of study and the medical surveillance performed, which included the type of nanomaterial, any exposure details provided, as well as health indicators and biomarkers tested.</p><p>Results</p><p>Initially 92 studies were identified, from which 84 full texts were assessed for eligibility. Seven studies met all the inclusion criteria, i.e. those performed in Taiwan, Korea, Czech Republic and the US. Of these, six compared health indicators between exposed and unexposed workers and one study described a surveillance program. All studies were at a high risk of bias. Workers were exposed to a mix of nanomaterials in three studies, carbon-based nanomaterials in two studies, nano-silver in one study and nano-titanium oxide in the other study. Two studies did not find a difference in biomarkers between exposed and unexposed workers. In addition, differences in early effects on pulmonary function or neurobehavioral tests were not observed. One study found an increased prevalence of allergic dermatitis and “sneezing” in the exposed group.</p><p>Conclusions</p><p>This review of recently published data on surveillance studies proves that there is a gap in the current knowledge, where most of the surveillance-related studies reported do not follow a set format that provides the required information on ENM characterisation, the type of exposure and the measured indicators/biomarkers. Hence, there is very low quality evidence that screening and surveillance might detect adverse health effects associated with workplace exposure. This systematic review is relevant because it proves that, although surveillance programs have been initiated and preliminary results are being published, the current studies are actually not answering the important questions or solving the overall problem regarding what the potential health hazards are among workers either handling or potentially exposed to ENMs. The recommendations, thus proposed, are based on an obvious need for (i) exposure registries, where longitudinal follow-up studies should inform surveillance, (ii) known exposure measurements or summary indices for ENMs as a reference (iii) validation of candidate biomarkers and (iv) studies that compare the effects of these surveillance approaches to usual care, e.g. those commonly followed for bulk-size hazardous materials.</p></div

Gold Nanoparticle Interference Study during the Isolation, Quantification, Purity and Integrity Analysis of RNA

<div><p>Investigations have been conducted regarding the interference of nanoparticles (NPs) with different toxicological assay systems, but there is a lack of validation when conducting routine tests for nucleic acid isolation, quantification, integrity, and purity analyses. The interference of citrate-capped gold nanoparticles (AuNPs) was investigated herein. The AuNPs were added to either BEAS-2B bronchial human cells for 24 h, the isolated pure RNA, or added during the isolation procedure, and the resultant interaction was assessed. Total RNA that was isolated from untreated BEAS-2B cells was spiked with various concentrations (v/v%) of AuNPs and quantified. A decrease in the absorbance spectrum (220–340 nm) was observed in a concentration-dependent manner. The 260 and 280 nm absorbance ratios that traditionally infer RNA purity were also altered. Electrophoresis was performed to determine RNA integrity, but could not differentiate between AuNP-exposed samples. However, the spiked post-isolation samples did produce differences in spectra (190–220 nm), where shifts were observed at a shorter wavelength. These shifts could be due to alterations to chromophores found in nucleic acids. The co-isolation samples, spiked with 100 µL AuNP during the isolation procedure, displayed a peak shift to a longer wavelength and were similar to the results obtained from a 24 h AuNP treatment, under non-cytotoxic test conditions. Moreover, hyperspectral imaging using CytoViva dark field microscopy did not detect AuNP spectral signatures in the RNA isolated from treated cells. However, despite the lack of AuNPs in the final RNA product, structural changes in RNA could still be observed between 190–220 nm. Consequently, full spectral analyses should replace the traditional ratios based on readings at 230, 260, and 280 nm. These are critical points of analyses, validation, and optimization for RNA-based techniques used to assess AuNPs effects.</p></div

Description of included studies.

<p>Description of included studies.</p

RNA integrity analysis.

<p>(<b>A</b>) Post-isolation spiked samples. (<b>B</b>) Co-isolation spiked samples. Lanes: (<b>1</b>) RNA untreated control. (<b>2</b>) RNA untreated control with RNAProtect solution +25% AuNP-spike. (<b>3</b>) RNA untreated control with RNAProtect solution +50% AuNP-spike. (<b>4</b>) RNA untreated control with RNAProtect solution +75% AuNP-spike. (<b>5</b>) AuNP (3 nM) with 6xOrange Loading dye (Fermentas). (<b>6</b>) The 24 h AuNP-treated RNA with RNAProtect solution. (<b>7</b>) RNA untreated control. (<b>8</b>) RNA untreated control +25 µL AuNP-spike. (<b>9</b>) RNA untreated control +50 µL AuNP-spike. (<b>10</b>) RNA untreated control +100 µL AuNP-spike. (<b>11</b>) Unloaded lane. (<b>12</b>) RNA untreated control with RNAProtect solution (<b>13</b>) RNA untreated control with RNAProtect solution +25 µL AuNP-spike. (<b>14</b>) RNA untreated control with RNAProtect solution +50 µL AuNP-spike. (<b>15</b>) RNA untreated control with RNAProtect solution +100 µL AuNP-spike. (<b>16</b>) Unloaded lane. (<b>17</b>) AuNP (3 nM) with 6xOrange Loading dye (Fermentas).</p

Study overview of included and excluded papers.

<p>Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166071#pone.0166071.s001" target="_blank">S1 Table</a> for exclusion reasons per citation. Note: One study was excluded because full text was not available [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166071#pone.0166071.ref024" target="_blank">24</a>].</p

Summary of study bias.

<p>Summary of study bias.</p

UV-Vis spectroscopy of RNA from post-isolation spiked samples.

<p>(<b>A</b>) Full spectrum absorbance analyses of artificial AuNP-spikes, measured at wavelengths from 190–840 nm. (<b>B</b>) Peak shifts of absorption spectra of artificial AuNP-spikes, measured at wavelengths from 190–235 nm. (<b>C</b>) Traditional absorbance spectrum analyses of artificial AuNP-spikes, measured at wavelengths from 220–340 nm. (<b>D</b>) Absorption spectra of artificial AuNP-spikes, measured at wavelengths from 450–600 nm. (<b>E</b>) Spiked samples containing a constant amount of RNA with variable percentage of AuNPs, indicating the absorption spectra measured at wavelengths from 190–235 nm.</p

UV absorption bands for chromophores, adapted from [29].

<p>*The extinction coefficient <i>ε</i>  =  M_r.(A/cl), and is related to the relative molecular mass, M_r.</p><p>UV absorption bands for chromophores, adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114123#pone.0114123-Phillips1" target="_blank">[29]</a>.</p