Qualitative and quantitative simulation of best management practices (BMPs) for contaminated megasite remediation using the SiteWise™ tool.

Remediation activities, particularly in megasites, may induce substantial secondary environmental impacts that must be addressed for green and sustainable remediation (GSR) practices. Only limited studies are available quantitatively assessing the environmental footprint and environmental benefits of implementing Best Management Practices (BMPs) in megasite remediation. This study used the SiteWise™ tool, a quantitative environmental footprint assessment for scenario simulation and benefit quantification of BMPs, on a contaminated megasite in Hebei Province, China. We observed a considerable environmental footprint and energy from the remediation. Taking the final implementation alternative (Alt 1) as an example, which is characterized by combining multiple remediation techniques, the greenhouse gas (GHG) emissions reached 113,474 t, the energy used was 2,082,841 million metric British thermal units (MMBTU), and other air pollutant emissions (NOx, SOx, and PM10) amounted to 856 t. Further BMP analyses highlighted the benefits of substituting the conventional solidification/stabilization agent with willow woodchip-based biochar, which could reduce GHG emissions by 50,806 t and energy used by 926,648 MMBTU. The overall environmental benefits of implementing all applicable BMPs in the remediation were significant, with a 66.85%, 50.15%, and 56.05% reduction in GHG emissions, energy used, and other air pollutants, respectively. Our study provides insights into quantifying the environmental footprint and exploring emission reduction pathways for contaminated megasite remediation. It also offers a feasible path for quantifying the environmental benefits of BMPs, promoting the development of GSR of contaminated sites.

Mechanically Regulated Outside-In Activation of an I-Domain-Containing Integrin.

Integrins are heterodimeric transmembrane proteins that mediate cellular adhesion and bidirectional mechanotransductions through their conformational allostery. The allosteric pathway of an I-domain-containing integrin remains unclear because of its complexity and lack of effective experiments. For a typical I-domain-containing integrin αXß2, molecular dynamics simulations were employed here to investigate the conformational dynamics in the first two steps of outside-in activation, the bindings of both the external and internal ligands. Results showed that the internal ligand binding is a prerequisite to the allosteric transmission from the α- to ß-subunits and the exertion of external force to integrin-ligand complex. The opening state of αI domain with downward movement and lower half unfolding of α7-helix ensures the stable intersubunit conformational transmission through external ligand binding first and internal ligand binding later. Reverse binding order induces a, to our knowledge, novel but unstable swingout of ß-subunit Hybrid domain with the retained close states of both αI and ßI domains. Prebinding of external ligand greatly facilitates the following internal ligand binding and vice versa. These simulations furthered the understanding in the outside-in activation of I-domain-containing integrins from the viewpoint of internal allosteric pathways.

Distinct binding affinities of Mac-1 and LFA-1 in neutrophil activation.

Macrophage-1 Ag (Mac-1) and lymphocyte function-associated Ag-1 (LFA-1), two ß2 integrins expressed on neutrophils (PMNs), mediate PMN recruitment cascade by binding to intercellular adhesive molecule 1. Distinct functions of LFA-1-initiating PMN slow rolling and firm adhesion but Mac-1-mediating cell crawling are assumed to be governed by the differences in their binding affinities and kinetic rates. In this study, we applied an adhesion frequency approach to compare their kinetics in the quiescent and activated states using three molecular systems, constitutively expressed receptors on PMNs, wild-type and high-affinity (HA) full-length constructs transfected on 293T cells, and wild-type and HA recombinant extracellular constructs. Data indicate that the difference in binding affinity between Mac-1 and LFA-1 is on-rate dominated with slightly or moderately varied off-rate. This finding was further confirmed when both ß2 integrins were activated by chemokines (fMLF or IL-8), divalent cations (Mg(2+) or Mn(2+)), or disulfide bond lockage on an HA state. Structural analyses reveal that such the kinetics difference is likely attributed to the distinct conformations at the interface of Mac-1 or LFA-1 and intercellular adhesive molecule 1. This work furthers the understandings in the kinetic differences between Mac-1 and LFA-1 and in their biological correlations with molecular activation and structural bases.

Transport of Amino Acids in Soy Sauce Desalination Process by Electrodialysis.

Soy sauce is a common condiment that has a unique flavor, one that is derived from its rich amino acids and salts. It is known that excessive intake of high-sodium food will affect human health, causing a series of diseases such as hypertension and kidney disease. Therefore, removing sodium from the soy sauce and retaining the amino acids is desirable. In this study, electrodialysis (ED) was employed for the desalination of soy sauce using commercial ion exchange membranes (IEMs). The influence of the current density and initial pH on the desalination degree of the soy sauce was explored. Results showed that the optimal desalination condition for ED was reached at a current density of 5 mA/cm2 and pH of 5, with the desalination degree of 64% and the amino acid loss rate of 29.8%. Moreover, it was found that the loss rate of amino acids was related to the initial concentration and molecular structure. In addition, the amino acid adsorption by IEMs was explored. Results implied that the molecular weight and structure affect amino acid adsorption. This study illustrated that the ED process can successfully reduce the salt content of the soy sauce and retain most of the amino acids without compromising the original flavor.

High-performance liquid chromatography fractionation using a silver-modified column followed by two-dimensional comprehensive gas chromatography for detailed group-type characterization of oils and oil pollutions.

Successful remediation of oil-contaminated soils relies on a sound preceding characterization of the oil chemical composition and physicochemical properties. Comprehensive two-dimensional gas chromatography with flame ionization detection (GCxGC/FID) is known to be very suitable for the analysis of complex samples such as petroleum hydrocarbons. However, in spite of the high-separation power offered by GCxGC, it fails to completely separate certain hydrocarbon groups in petroleum hydrocarbon mixtures. This hampers a detailed chemical composition assessment which can lead to wrong conclusions on the behaviour of the oil in soil systems, e.g. biological degradability and water solubility. This paper describes a high-performance liquid chromatography (HPLC) system with a silver-modified column as a prefractionation step to GCxGC to improve chemical identification. With HPLC, the petroleum hydrocarbons were baseline separated into a saturated fraction (including alkanes and cycloalkanes) and an unsaturated fraction (including alkenes, aromatic hydrocarbons and heterocyclic components). Each fraction eluted in a small time window limiting the dilution caused by HPLC. The two fractions were collected and quantitatively analyzed with GCxGC/FID. Cold splitless injection of 4 microl was adopted to compensate the dilution caused by the prefractionation step. With oil-spiked soil samples, a good reproducibility was obtained (RSD=3.5%; n=7) and the recovery was satisfactory (87.7%).

Salt bridge interactions within the ß2 integrin α7 helix mediate force-induced binding and shear resistance ability.

The functional performance of the αI domain α7 helix in ß2 integrin activation depends on the allostery of the α7 helix, which axially slides down; therefore, it is critical to elucidate what factors regulate the allostery. In this study, we determined that there were two conservative salt bridge interaction pairs that constrain both the upper and bottom ends of the α7 helix. Molecular dynamics (MD) simulations for three ß2 integrin members, lymphocyte function-associated antigen-1 (LFA-1; αL ß2 ), macrophage-1 antigen (Mac-1; αM ß2 ) and αx ß2 , indicated that the magnitude of the salt bridge interaction is related to the stability of the αI domain and the strength of the corresponding force-induced allostery. The disruption of the salt bridge interaction, especially with double mutations in both salt bridges, significantly reduced the force-induced allostery time for all three members. The effects of salt bridge interactions of the αI domain α7 helix on ß2 integrin conformational stability and allostery were experimentally validated using Mac-1 constructs. The results demonstrated that salt bridge mutations did not alter the conformational state of Mac-1, but they did increase the force-induced ligand binding and shear resistance ability, which was consistent with MD simulations. This study offers new insight into the importance of salt bridge interaction constraints of the αI domain α7 helix and external force for ß2 integrin function.

Contribution of the CR domain to P-selectin lectin domain allostery by regulating the orientation of the EGF domain.

The allostery of P-selectin has been studied extensively with a focus on the Lec and EGF domains, whereas the contribution of the CR domain remains unclear. Here, molecular dynamics simulations (MDS) combined with homology modeling were preformed to investigate the impact of the CR domain on P-selectin allostery. The results indicated that the CR domain plays a role in the allosteric dynamics of P-selectin in two ways. First, the CR1 domain tends to stabilize the low affinity of P-selectin during the equilibration processes with the transition inhibition from the S1 to S1' state by restraining the extension of the bent EGF orientation, or with the relaxation acceleration of the S2 state by promoting the bending of the extended EGF orientation. Second, the existence of CR domain increases intramolecular extension prior to complex separation, increasing the time available for the allosteric shift during forced dissociation with a prolonged bond duration. These findings further our understanding of the structure-function relationship of P-selectin with the enriched micro-structural bases of the CR domain.

Mechanomics: an emerging field between biology and biomechanics.

Cells sense various in vivo mechanical stimuli, which initiate downstream signaling to mechanical forces. While a body of evidences is presented on the impact of limited mechanical regulators in past decades, the mechanisms how biomechanical responses globally affect cell function need to be addressed. Complexity and diversity of in vivo mechanical clues present distinct patterns of shear flow, tensile stretch, or mechanical compression with various parametric combination of its magnitude, duration, or frequency. Thus, it is required to understand, from the viewpoint of mechanobiology, what mechanical features of cells are, why mechanical properties are different among distinct cell types, and how forces are transduced to downstream biochemical signals. Meanwhile, those in vitro isolated mechanical stimuli are usually coupled together in vivo, suggesting that the different factors that are in effect individually could be canceled out or orchestrated with each other. Evidently, omics analysis, a powerful tool in the field of system biology, is advantageous to combine with mechanobiology and then to map the full-set of mechanically sensitive proteins and transcripts encoded by its genome. This new emerging field, namely mechanomics, makes it possible to elucidate the global responses under systematically-varied mechanical stimuli. This review discusses the current advances in the related fields of mechanomics and elaborates how cells sense external forces and activate the biological responses.

Conformational stability analyses of alpha subunit I domain of LFA-1 and Mac-1.

ß2 integrin of lymphocyte function-associated antigen-1 (LFA-1) or macrophage-1 antigen (Mac-1) binds to their common ligand of intercellular adhesion molecule-1 (ICAM-1) and mediates leukocyte-endothelial cell (EC) adhesions in inflammation cascade. Although the two integrins are known to have distinct functions, the corresponding micro-structural bases remain unclear. Here (steered-)molecular dynamics simulations were employed to elucidate the conformational stability of α subunit I domains of LFA-1 and Mac-1 in different affinity states and relevant I domain-ICAM-1 interaction features. Compared with low affinity (LA) Mac-1, the LA LFA-1 I domain was unstable in the presence or absence of ICAM-1 ligand, stemming from diverse orientations of its α7-helix with different motifs of zipper-like hydrophobic junction between α1- and α7-helices. Meanwhile, spontaneous transition of LFA-1 I domain from LA state to intermediate affinity (IA) state was first visualized. All the LA, IA, and high affinity (HA) states of LFA-1 I domain and HA Mac-1 I domain were able to bind to ICAM-1 ligand effectively, while LA Mac-1 I domain was unfavorable for binding ligand presumably due to the specific orientation of S144 side-chain that capped the MIDAS ion. These results furthered our understanding in correlating the structural bases with their functions of LFA-1 and Mac-1 integrins from the viewpoint of I domain conformational stability and of the characteristics of I domain-ICAM-1 interactions.

Estimation of ecotoxicity of petroleum hydrocarbon mixtures in soil based on HPLC-GCXGC analysis.

Detailed HPLC-GCXGC/FID (high performance liquid chromatography followed by comprehensive two-dimensional gas chromatography with flame-ionization detection) analysis of oil-contaminated soils was performed to interpret results of selected acute ecotoxicity assays. For the five ecotoxicity assays tested, plant seed germination and Microtox were selected as most sensitive for evaluating ecotoxicity of the oil in the soil phase and in the leaching water, respectively. The measured toxicity for cress when testing the soil samples did not correspond to TPH concentration in the soil. A detailed chemical composition analysis of the oil contamination using HPLC-GCXGC/FID allows to better predict the ecotoxicological risk and leaching potential of petroleum hydrocarbons in soil. Cress biomass production per plant was well correlated to the total aromatic hydrocarbon concentration (R2=0.79, n=6), while cress seed germination was correlated (R2=0.82, n=6) with total concentration of "highly water-soluble aromatic hydrocarbons" (HSaromatics). The observed ecotoxicity of the leaching water for Microtox-bacteria related well to calculated (based on the HPLC-GCXGC/FID results) petroleum hydrocarbon equilibrium concentrations in water.

Combining HPLC-GCXGC, GCXGC/ToF-MS, and selected ecotoxicity assays for detailed monitoring of petroleum hydrocarbon degradation in soil and leaching water.

HPLC-GCXGC/FID (high-performance liquid chromatography followed by comprehensive two-dimensional gas chromatography with flame-ionization detection) and GCXGC/ToF-MS (comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry) were used to study the biodegradation of petroleum hydrocarbons in soil microcosms during 20 weeks. Two soils were studied: one spiked with fresh diesel and one field sample containing weathered diesel-like oil. Nutrient amended and unamended samples were included. Total petroleum hydrocarbon (TPH) levels in spiked soil decreased from 15,000 to 7,500 mg/kg d.m. and from 12,0O0 to 4,000 mg/kg d.m. in the field soil. Linear alkanes and aromatic hydrocarbons were better biodegradable (>60% degraded) than iso-alkanes; cycloalkanes were least degradable (<40%). Aromatic hydrocarbons up to three rings showed better degradability than n-alkanes. GCXGC/ToF-MS analysis of leaching water showed that initially various oxygenated hydrocarbons were produced. Compound peaks seemed to move up and rightward in the GCXGC chromatograms, indicating that more polar and heavier compounds were formed as biodegradation proceeded. Nutrient amendment can increase TPH removal rates, but had adverse effects on ecotoxicity and leaching potential in our experiment This was explained by observed shifts in the soil microbial community. Ecotoxicity assays showed that residual TPH still inhibited cress (Lepidium sativum) seed germination, but the leaching water was no longer toxic toward luminescent bacteria (Vibrio fischeri).

Aqueous solubility calculation for petroleum mixtures in soil using comprehensive two-dimensional gas chromatography analysis data.

An assessment of aqueous solubility (leaching potential) of soil contaminations with petroleum hydrocarbons (TPH) is important in the context of the evaluation of (migration) risks and soil/groundwater remediation. Field measurements using monitoring wells often overestimate real TPH concentrations in case of presence of pure oil in the screened interval of the well. This paper presents a method to calculate TPH equilibrium concentrations in groundwater using soil analysis by high-performance liquid chromatography followed by comprehensive two-dimensional gas chromatography (HPLC-GCXGC). The oil in the soil sample is divided into 79 defined hydrocarbon fractions on two GCXGC color plots. To each of these fractions a representative water solubility is assigned. Overall equilibrium water solubility of the non-aqueous phase liquid (NAPL) present in the sample and the water phase's chemical composition (in terms of the 79 fractions defined) are then calculated using Raoult's law. The calculation method was validated using soil spiked with 13 different TPH mixtures and 1 field-contaminated soil. Measured water solubilities using a column recirculation equilibration experiment agreed well to calculated equilibrium concentrations and water phase TPH composition.

Detailed analysis of petroleum hydrocarbon attenuation in biopiles by high-performance liquid chromatography followed by comprehensive two-dimensional gas chromatography.

Enhanced bioremediation of petroleum hydrocarbons in two biopiles was quantified by high-performance liquid chromatography (HPLC) followed by comprehensive two-dimensional gas chromatography (GCXGC). The attenuation of 34 defined hydrocarbon classes was calculated by HPLC-GCXGC analysis of representative biopile samples at start-up and after 18 weeks of biopile operation. In general, a-cyclic alkanes were most efficiently removed from the biopiles, followed by monoaromatic hydrocarbons. Cycloalkanes and polycyclic aromatic hydrocarbons (PAHs) were more resistant to degradation. A-cyclic biomarkers farnesane, trimethyl-C13, norpristane, pristane and phytane dropped to only about 10% of their initial concentrations. On the other hand, C29-C31 hopane concentrations remained almost unaltered after 18 weeks of biopile operation, confirming their resistance to biodegradation. They are thus reliable indicators to estimate attenuation potential of petroleum hydrocarbons in biopile processed soils.