Health Risk-Based Assessment and Management of Heavy Metals-Contaminated Soil Sites in Taiwan

Risk-based assessment is a way to evaluate the potential hazards of contaminated sites and is based on considering linkages between pollution sources, pathways, and receptors. These linkages can be broken by source reduction, pathway management, and modifying exposure of the receptors. In Taiwan, the Soil and Groundwater Pollution Remediation Act (SGWPR Act) uses one target regulation to evaluate the contamination status of soil and groundwater pollution. More than 600 sites contaminated with heavy metals (HMs) have been remediated and the costs of this process are always high. Besides using soil remediation techniques to remove contaminants from these sites, the selection of possible remediation methods to obtain rapid risk reduction is permissible and of increasing interest. This paper discusses previous soil remediation techniques applied to different sites in Taiwan and also clarified the differences of risk assessment before and after soil remediation obtained by applying different risk assessment models. This paper also includes many case studies on: (1) food safety risk assessment for brown rice growing in a HMs-contaminated site; (2) a tiered approach to health risk assessment for a contaminated site; (3) risk assessment for phytoremediation techniques applied in HMs-contaminated sites; and (4) soil remediation cost analysis for contaminated sites in Taiwan

Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.

Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher's fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life

Encapsulation of ribozymes inside model protocells leads to faster evolutionary adaptation.

Functional biomolecules, such as RNA, encapsulated inside a protocellular membrane are believed to have comprised a very early, critical stage in the evolution of life, since membrane vesicles allow selective permeability and create a unit of selection enabling cooperative phenotypes. The biophysical environment inside a protocell would differ fundamentally from bulk solution due to the microscopic confinement. However, the effect of the encapsulated environment on ribozyme evolution has not been previously studied experimentally. Here, we examine the effect of encapsulation inside model protocells on the self-aminoacylation activity of tens of thousands of RNA sequences using a high-throughput sequencing assay. We find that encapsulation of these ribozymes generally increases their activity, giving encapsulated sequences an advantage over nonencapsulated sequences in an amphiphile-rich environment. In addition, highly active ribozymes benefit disproportionately more from encapsulation. The asymmetry in fitness gain broadens the distribution of fitness in the system. Consistent with Fisher's fundamental theorem of natural selection, encapsulation therefore leads to faster adaptation when the RNAs are encapsulated inside a protocell during in vitro selection. Thus, protocells would not only provide a compartmentalization function but also promote activity and evolutionary adaptation during the origin of life

ESR study of interfacial hydration layers of polypeptides in water-filled nanochannels and in vitrified bulk solvents.

There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1~7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ~0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ~2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration

Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis.

The identification of catalytic RNAs is typically achieved through primarily experimental means. However, only a small fraction of sequence space can be analyzed even with high-throughput techniques. Methods to extrapolate from a limited data set to predict additional ribozyme sequences, particularly in a human-interpretable fashion, could be useful both for designing new functional RNAs and for generating greater understanding about a ribozyme fitness landscape. Using information theory, we express the effects of epistasis (i.e., deviations from additivity) on a ribozyme. This representation was incorporated into a simple model of the epistatic fitness landscape, which identified potentially exploitable combinations of mutations. We used this model to theoretically predict mutants of high activity for a self-aminoacylating ribozyme, identifying potentially active triple and quadruple mutants beyond the experimental data set of single and double mutants. The predictions were validated experimentally, with nine out of nine sequences being accurately predicted to have high activity. This set of sequences included mutants that form a previously unknown evolutionary bridge between two ribozyme families that share a common motif. Individual steps in the method could be examined, understood, and guided by a human, combining interpretability and performance in a simple model to predict ribozyme sequences by extrapolation

Long-range water accessibility study by ESE.

<p>The theoretical fits (red lines) to the ESE experimental data (blue lines) using a stretched exponential function (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068264#pone-0068264-t001" target="_blank">Table 1</a>) as previously described. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068264#pone.0068264-Huang1" target="_blank">[11]</a> The results for the n3β-s and PPm3-s are shown in (a) and (b), respectively. The decay signals acquired by the ESE experiments were fitted over the maxima of the deuterium modulation as described in Zecevic et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068264#pone.0068264-Zecevic1" target="_blank">[32]</a> to minimize the influence from destructive interference of nuclear modulations. The obtained values of the T_M (in ns) and stretching exponent x are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068264#pone-0068264-t001" target="_blank">Table 1</a>. The T_M values can be directly used to yield the surrounding proton density (<i>C_ex</i>; cf. Eq. 2) within the range of ∼2 nm from a nitroxide spin.</p

Parameters obtained in the analyses of the ESE and ESEEM data.^§

§<p>Estimated errors: 5%(T_M), 10%(x), 13% (<i>C_ex</i>), 5% (<i>k_D</i>), 10% (Π). Abbreviations: <b>n3-s-a</b> (the n3-s is within SBA15a containing pure water); <b>n3-s-b</b> (the n3-s is within SBA15b containing pure water); <b>n3-s-sol(s)</b> (the n3-s is in a vitrified bulk solvent containing 40 wt% sucrose, (s), in D₂O or H₂O); <b>PPm3-s-sol(g)</b> (PPm3-s is in a vitrified bulk solvent containing 40v/v% glycerol in H₂O; deuterated glycerol is used if the solvent is D₂O, a condition of which is represented by sol(dg)/D₂O in main text); <b>PPm3-s-sol(s)</b> (PPm3-s is in a vitrified bulk solvent containing 40 wt% sucrose in D₂O or H₂O). In all of the experiments, the surface group of the nanochannels is modified to –SiOD in advance if D₂O is used. See Method for details.</p>#<p>The values of T_M and x are obtained in the analysis of the pulsed ESE measurements using a stretched exponential function, , where τ is the time between the two pulses, x the exponent, and Y(0) is the echo intensity at τ  = 0. The obtained values are used to yield <i>C_ex</i> using Eq. (2). The <i>C_ex</i> represents ESE-based water accessibility within the range of ∼2 nm from the nitroxide spin.</p>¶<p>The <i>k_D</i> values are obtained in the theoretical analysis of the ESEEM measurements as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0068264#pone-0068264-g003" target="_blank">Figure 3</a>. The best-fit values for the damping constant (<i>τ₀</i>) and phase (φ) are very close together (2.9∼3.0). The Π represents ESEEM-based water accessibility within the range of ∼0.35 nm from the nitroxide spin.</p

Determination of the n3α-d structure.

<p>(a) The time-domain DEER signals of the studied conditions. The gray lines represent the exponential baselines that best fit the data. Inset shows a ribbon model of the n3α-d derived from NMR data (PDB code: 1M25). (b) The P(r) distributions extracted from the time-domain DEER data by the Tikhonov regularization analysis. The average distances (∼2.0 nm) are consistent with the expectation. (c) The cw-ESR spectra of the n3α-d. The spectra of the bulk solution studies are characterized by a broader linewidth and the spectral heterogeneity (indicated by arrows) as compared to the spectra of the nanochannel studies.</p