Physicochemical Changes of Few-Layer Graphene in Peroxidase-Catalyzed Reactions: Characterization and Potential Ecological Effects

The environmental implications of graphene have received much attention, however, little is known about how graphene affects or may be affected by the enzymatic reactions that are critically involved in natural organic matter transformation processes. We conducted experiments to examine the role of few-layer graphene (FLG) in the reaction system of tetrabromobisphenol A (TBBPA) mediated by horseradish peroxidase (HRP). We found that TBBPA was transformed by HRP into two products that were likely formed from coupling of two TBBPA radicals via interaction of an oxygen atom on one radical and a propyl-substituted aromatic carbon atom on the other. Presence of FLG greatly increased the reaction rate by protecting HRP from inactivation. Direct reactions between TBBPA radicals and FLG were unequivocally evidenced using ¹⁴C labeling and the characteristic photoelectron response of bromine contained in TBBPA. The thickness, size, and aggregation profile of FLG was modified by the reaction as shown by multiple characterization tools. Assessment using <i>Daphnia magna</i> revealed a substantial decrease in the bioaccumulation and toxicity of the FLG after being modified. The data provides the first evidence that FLG can be modified in HRP-mediated reactions and indicates that such modifications may have strong implications in its ecological effects

Supplemental material for Two-way partial AUC and its properties

Supplemental Material for Two-way partial AUC and its properties by Hanfang Yang, Kun Lu, Xiang Lyu and Feifang Hu in Statistical Methods in Medical Research</p

Physicochemical Changes of Few-Layer Graphene in Peroxidase-Catalyzed Reactions: Characterization and Potential Ecological Effects

The environmental implications of graphene have received much attention, however, little is known about how graphene affects or may be affected by the enzymatic reactions that are critically involved in natural organic matter transformation processes. We conducted experiments to examine the role of few-layer graphene (FLG) in the reaction system of tetrabromobisphenol A (TBBPA) mediated by horseradish peroxidase (HRP). We found that TBBPA was transformed by HRP into two products that were likely formed from coupling of two TBBPA radicals via interaction of an oxygen atom on one radical and a propyl-substituted aromatic carbon atom on the other. Presence of FLG greatly increased the reaction rate by protecting HRP from inactivation. Direct reactions between TBBPA radicals and FLG were unequivocally evidenced using ¹⁴C labeling and the characteristic photoelectron response of bromine contained in TBBPA. The thickness, size, and aggregation profile of FLG was modified by the reaction as shown by multiple characterization tools. Assessment using <i>Daphnia magna</i> revealed a substantial decrease in the bioaccumulation and toxicity of the FLG after being modified. The data provides the first evidence that FLG can be modified in HRP-mediated reactions and indicates that such modifications may have strong implications in its ecological effects

Templating Molecular Arrays in Amyloid’s Cross-β Grooves

Amyloid fibers, independent of primary amino acid sequence, share a common cross-β structure and bind the histochemical dye Congo Red (CR). Despite extensive use of CR in amyloid diagnostics, remarkably little is known about the specific and characteristic binding interactions. Fibril insolubility, morphological inhomogeneity, and multiple possible ligand binding sites all conspire to limit characterization. Here, we have exploited the structure of cross-β nanotubes, which limit the number of potential binding sites, to directly interrogate cross-β laminate grooves. CR bound to cross-β nanotubes displays the hallmark apple-green interference color, a broad red-shifted low energy transition, and a Kd of 1.9 ± 0.5 μM. Oriented electron diffraction and linear dichroism defines the orientation of CR as parallel to the amyloid long axis and colinear with laminate grooves. The broad red-shifted UV signature of CR bound to amyloid can be explained by semiempirical quantum calculations that support the existence of a precise network of J- and H-CR aggregates, illuminating the ability of the amyloid to organize molecules into extended arrays that underlie the remarkable diagnostic potential of CR

Molecular Dosimetry of <i>N</i>²-Hydroxymethyl-dG DNA Adducts in Rats Exposed to Formaldehyde

In this study, both endogenous and exogenous N2-hydroxymethyl-dG adducts in nasal DNA of rats exposed to 0.7, 2, 5.8, 9.1, or 15.2 ppm [13CD2] formaldehyde for 6 h were quantified by a highly sensitive nano-UPLC-MS/MS method. Our data clearly demonstrated that exogenous formaldehyde DNA adducts form in a highly nonlinear fashion, with a 21.7-fold increase in exposure causing a 286-fold increase in exogenous adducts. The ratio of exogenous/endogenous DNA adducts demonstrated that endogenous DNA adducts dominated at low exposures, comprising more than 99%. In contrast, exogenous adducts were not detectable in the bone marrow of rats exposed to 15.2 ppm [13CD2] formaldehyde

Chronic Arsenic Exposure Perturbs Gut Microbiota and Bile Acid Homeostasis in Mice

Arsenic exposure can perturb gut microbiota and their metabolic functions. We exposed C57BL/6 mice to 1 ppm arsenic in drinking water and investigated whether arsenic exposure affects the homeostasis of bile acids, a group of key microbiome-regulated signaling molecules of microbiome–host interactions. We found that arsenic exposure differentially changed major unconjugated primary bile acids and consistently decreased secondary bile acids in the serum and liver. The relative abundance of Bacteroidetes and Firmicutes was associated with the bile acid level in serum. This study demonstrates that arsenic-induced gut microbiota dysbiosis may play a role in arsenic-perturbed bile acid homeostasis

Inactivation of Laccase by the Attack of As (III) Reaction in Water

Laccase is a multicopper oxidase containing four coppers as reaction sites, including one type 1, one type 2, and two type 3. We here provide the first experimental data showing that As (III) can be effectively removed from water and transformed to As (V) through reactions mediated by laccase with the presence of oxygen. To this end, the As (III) removal, As (V) yields, total protein, active laccase, and copper concentrations in the aqueous phase were determined, respectively. Additionally, electron paramagnetic resonance spectra and UV–vis spectra were applied to probe possible structural changes of the laccase during the reaction. The data offer the first evidence that laccase can be inactivated by As (III) attack thus leading to the release of type 2 copper. The released copper has no reactivity with the As (III). These findings provide new ideas into a significant pathway likely to master the environmental transformation of arsenite, and advance the understanding of laccase inactivation mechanisms, thus providing a foundation for optimization of enzyme-based processes and potential development for removal and remediation of arsenite contamination in the environment

Formation of <i>S-</i>[1-(<i>N</i>²-Deoxyguanosinyl)methyl]glutathione between Glutathione and DNA Induced by Formaldehyde

Formation of S-[1-(N2-Deoxyguanosinyl)methyl]glutathione between Glutathione and DNA Induced by Formaldehyd

Exploiting Amyloid Fibril Lamination for Nanotube Self-Assembly

Fundamental questions about the relative arrangement of the β-sheet arrays within amyloid fibrils remain central to both its structure and the mechanism of self-assembly. Recent computational analyses suggested that sheet-to-sheet lamination was limited by the length of the strand. On the basis of this hypothesis, a short seven-residue segment of the Alzheimer's disease-related Aβ peptide, Aβ(16−22), was allowed to self-assemble under conditions that maintained the basic amphiphilic character of Aβ. Indeed, the number increased over 20-fold to 130 laminates, giving homogeneous bilayer structures that supercoil into long robust nanotubes. Small-angle neutron scattering and X-ray scattering defined the outer and inner radii of the nanotubes in solution to contain a 44-nm inner cavity with 4-nm-thick walls. Atomic force microscopy and transmission electron microscopy images further confirmed these homogeneous arrays of solvent-filled nanotubes arising from a flat rectangular bilayer, 130 nm wide × 4 nm thick, with each bilayer leaflet composed of laminated β-sheets. The corresponding backbone H-bonds are along the long axis, and β-sheet lamination defines the 130-nm bilayer width. This bilayer coils to give the final nanotube. Such robust and persistent self-assembling nanotubes with positively charged surfaces of very different inner and outer curvature now offer a unique, robust, and easily accessible scaffold for nanotechnology