BINSIMDB: Benchmark Dataset Construction for Fine-Grained Binary Code Similarity Analysis
Explore the source record for details and available documents.
Zuo, Fei↗
Engineering topics
Zeng, Qiang
Publications and source records attributed to Zeng, Qiang.
BINSIMDB: Benchmark Dataset Construction for Fine-Grained Binary Code Similarity Analysis
Explore the source record for details and available documents.
Zuo, Fei↗
Inhibition of Extracellular Enzyme Activity by Reactive Oxygen Species upon Oxygenation of Reduced Iron-Bearing Minerals
The dual roles of minerals in inhibiting and prolonging extracellular enzyme activity in soils and sediments are governed by enzyme adsorption to mineral surface. Oxigenation of mineral-bound Fe(II) generates reactive oxygen species (ROS), yet it is unknown whether and how this process alters the activity and functional lifespan of extracellular enzymes. Here, the effect of mineral-bound Fe(II) oxidation on the hydrolytic activity of a cellulose-degrading enzyme ß-glucosidase (BG) was studied using two pre-reduced Fe-bearing clay minerals (nontronite and montmorillonite) and one pre-reduced iron oxide (magnetite) at pH 5 and 7. Under anoxic condition, BG adsorption to mineral surface decreased its activity but prolonged its lifespan. Under oxic condition, ROS was produced, with the amount of •OH, the most abundant ROS, being positively correlated with the extent of structural Fe(II) oxidation in reduced minerals. •OH decreased BG activity and shortened its lifespan via conformational change and structural decomposition of BG. These results suggest that under oxic condition the ROS-induced inhibitory role of Fe(II)-bearing minerals outweighed their adsorption-induced protective role in controlling enzyme activity. These results disclose a previously unknown mechanism of extracellular enzyme inactivation, which have pivotal implications for predicting the active enzyme pool in redox-oscillating environments.
58 GEOSCIENCES↗
Effect of bacterial cell addition on Fe(III) reduction and soil organic matter transformation in a farmland soil
The coupled biogeochemical processes of Fe(III) reduction and organic matter transformation profoundly impact terrestrial carbon cycling. However, little is known about the microbial role in soil organic matter (SOM) transformation during Fe(III) bio-reduction. Here we investigated the bio-reduction behavior of a black farmland soil and corresponding SOM transformation under circumneutral and anoxic conditions. A model dissimilatory Fe reducing bacterium, Geobacter sulfurreducens, was added in either live or dead form in order to enhance Fe(III) reduction in soil and to evaluate the accompanying transformation of SOM. The progress of Fe reduction was monitored and SOM transformation was characterized by various spectroscopy methods. Results showed that addition of either dead or live G. sulfurreducens cells increased the Fe(III) reduction rate and extent. Without cell addition, SOM transformation was insignificant within 13 days of incubation, only with some consumption of aliphatic/protein compounds, apparently due to their higher bio-degradability. Addition of dead or live cells resulted in more drastic SOM transformation, but through different mechanisms. With dead cell amendment, cell necromass and debris stimulated the activity of indigenous soil microbes by serving as extra carbon/energy sources. During Fe(III) reduction, the aliphatic/protein compounds were preferentially consumed by indigenous microbial communities, similar to the treatment without cell addition but with a greater extent of consumption. In comparison, addition of live G. sulfurreducens cells stimulated degradation of less bioavailable compounds, including more saturated and higher molecular weight SOM. It is possible that fast depletion of labile SOM by live G. sulfurreducens cells favored utilization of less bioavailable molecules (such as those with more aromatic structures) by the originally dormant species in native microbial community, suggesting an active role of live Fe(III)-reducing bacteria in affecting SOM transformation. In addition, fast assimilation of microbial related carbon, such as aromatic proteins and microbial byproducts, into SOM pools was also observed. Overall, our results suggest that addition of Fe(III)-reducing bacteria to a native soil can enhance Fe(III) reduction and accelerate the turnover of SOM through various mechanisms. The study provides new insights into coupled Fe(III) reduction and SOM transformation, as well as the “priming effect” of SOM using microbial cells as substrate.
54 ENVIRONMENTAL SCIENCES↗
Incremental rotary rolling mill and method
A rolling mill system for Incremental rotary shaping of an elongated workpiece is provided that includes first and second workpiece holders. A support frame has a track with the first and second workpiece holders being movably associated with the track, the workpiece holders and an associated workpiece being movable in unison along the track. A radial chuck is mounted to the frame that includes a plurality of jaws that are movable radially inwardly and outwardly. Each jaw has a tool mounted thereto that is rotatable about an axis of rotation, with the axis of rotation of each tool being oriented at a skew angle relative to the longitudinal axis of a workpiece. A source of electric current and an electrically conductive flow path are provided for flowing electrical current through a workpiece. A controller is provided that is configured to control the operation of each of the first motor, second motor and third motor, and to control the flow of current flowing through the tools to the workpiece.
Zeng, Qiang↗
Lignin-enhanced reduction of structural Fe(III) in nontronite: Dual roles of lignin as electron shuttle and donor
Lignin is a major component of plant-derived soil organic matter (SOM) in soils and sediments. Fe-bearing clay minerals are widely distributed in these environments and often co-exist with lignin. While previous studies have reported the electron shuttling and donating roles of certain redox-active SOM in the dissimilatory reduction of structural Fe(III) in Fe-bearing clay minerals, the role of lignin in this process remains unknown. Here we studied this role by incubating an Fe-rich smectite (nontronite NAu-2) with two types of lignin (soluble and insoluble) in the absence and presence of an Fe(III)-reducing bacterium Shewanella putrefaciens CN32 under anaerobic condition. Labile carbon source (i.e., lactate) was added in some experiments as an extra electron donor. The results demonstrated that both soluble and insoluble lignins abiotically reduced structural Fe(III) in NAu-2. The reduction extent was proportional to lignin concentration. After abiotic reaction, lignin served as either electron shuttle or electron donor in the presence of CN32: (1) When lactate was present, lignin served as an electron shuttle to enhance the rate of Fe(III) reduction; (2) When lactate was absent, lignin served as an electron donor for Fe(III) reduction. Although the biotic Fe(III) reduction extents were similar in the presence of either soluble or insoluble lignin, the reduction rates with soluble lignin were always higher than those with insoluble lignin, likely owing to their different electron transfer mechanisms. After interaction with NAu-2 and/or CN32, soluble lignin structure largely remained intact, but with some decreases of humic/fulvic acid-like and protein-like compounds, aromatic functional groups (e.g., C-H, C=O, COOH), and aliphatic/aromatic compounds. An increase of semiquinone-like organic radicals was observed after lignin interaction with NAu-2. These chemical changes of lignin were likely coupled with reduction of structural Fe(III) in nontronite. The nontronite structure remained largely unchanged without much dissolution and mineral transformation. The findings of this study provide insights into the role of lignin in promoting mineral-microbe interactions and have significant implications for coupled Fe and C biogeochemical cycles in soils and sediments.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantifying the anomalous water absorption behavior of cement mortar in view of its physical sensitivity to water
The one-dimensional water absorption into cement-based materials, possibly the simplest case of unsaturated water flow playing a fundamental role in predicting mass transport and durability, is still far from being completely understood due to several puzzling anomalies. Considering the water sensitivity of C-S-H gels (swell upon wetting and contract upon drying), a modified Richards equation (MRE) is proposed to quantify the anomalous water absorption into cement-based materials of changing porosity. Consistent experimental tests on a cement mortar and calculations indicate that the MRE with time-decaying water permeability can quantitatively capture the long-term absorption with two linear stages and a nonlinear transition stage between them. The water sensitivity is validated to be responsible for the anomalous deviation of water absorption from the classical square root of time law. It also partially contributes to the anomalous dependence of sorptivity on the temperature-dependent surface tension and viscosity of water and many organic liquids.
36 MATERIALS SCIENCE↗
Molecular Determination of Organic Adsorption Sites on Smectite during Fe Redox Processes Using ToF-SIMS Analysis
Turnover of soil organic carbon (SOC) is strongly affected by a balance between mineral protection and microbial degradation. However, the mechanisms controlling the heterogeneous and preferential adsorption of different types of SOC remain elusive, especially for humic substrates (HSs) and microbial carbon (MC), two hotly-debated forms of SOC prevalent in soils. In this work, the heterogeneous adsorption of HSs and MC on a clay mineral (nontronite NAu-2) during microbial-mediated Fe redox cycling was determined with the use of time-of-flight secondary ion mass spectrometry (ToF-SIMS). The results revealed that HSs pre-adsorbed on NAu-2 would partially inhibit the microbial Fe(III) reduction and structural modification of NAu-2, thus retarding the subsequent adsorption of MC. In contrast, NAu-2 without pre-coated HSs was adsorbed by a significant amount of MC from microbial polysaccharides as a result of Fe(III) reduction. This was attributed to the deposition of a thin Al-rich layer on clay surface, which provided active sites for MC adsorption. This study provides direct and detailed molecular evidence for the first time to explain the preferential adsorption of MC over HSs on the surface of clay minerals in the iron redox processes, which could be critical for the preservation of MC in soil. The results also indicate that ToF-SIMS is a unique tool for understanding complex organic-mineral-microbe interactions.
54 ENVIRONMENTAL SCIENCES↗
Role of clay-associated humic substances in catalyzing bioreduction of structural Fe(III) in nontronite by Shewanella putrefaciens CN32
Previous studies have shown that humic substances can serve as electron shuttle to catalyze bioreduction of structural Fe(III) in clay minerals, but it is unclear if clay-sorbed humic substances can serve the same function. It is unknown if the electron shuttling function is dependent on electron donor type and if humic substances undergo change as a result. Here, humic acid (HA) and fulvic acid (FA) were sorbed onto nontronite (NAu-2) surface. Structural Fe(III) in HA- and FA-coated NAu-2 samples was bioreduced by Shewanella putrefaciens CN32 using H 2 and lactate as electron donors. The results showed a contrasting effect of humic substances on bioreduction of structural Fe(III), depending on the electron donor type. With H 2 as electron donor, humic substances had little effect on bioreduction of Fe(III) (the reduction extent: 26.2%, 27.4%, 29.3% for HA-coated, FA-coated, and uncoated NAu-2, respectively). In contrast, these substances significantly enhanced bioreduction of Fe(III) with lactate as electron donor (the reduction extent: 20.2%, 20.7%, 11.5% for HA-coated, FA-coated, and uncoated NAu-2, respectively). This contrasting behavior is likely caused by the difference in reaction free energy and electron transport process between H 2 and lactate. When H 2 served as electron donor, more energy was released than when lactate served as electron donor. In addition, because of different cellular locations of lactate dehydrogenase (inner membrane) and H 2 hydrogenase (the periplasm), electrons generated by H 2 hydrogenase may pass through the electron transport chain more rapidly than those generated from lactate dehydrogenase. Through their functions as electron shuttle and/or carbon source, clay-sorbed HA/FA underwent partial transformation to amino acids and other compounds. The availability of external carbon source played an important role in the amount and type of secondary product generation. These results have important implications for coupled iron and carbon biogeochemical cycles in clay- and humic substance-rich environments.
54 ENVIRONMENTAL SCIENCES↗
Bio-reduction of ferrihydrite-montmorillonite-organic matter complexes: Effect of montmorillonite and fate of organic matter
Organic matter (OM) is often associated with Fe (hydr)oxides such as ferrihydrite (Fh) in soils and sediments, forming binary Fh-OM complexes. Microbial reduction of Fh results in destabilization of the complexes and mineral/OM transformation. However, little is known about the role of clay minerals in such processes, despite their common co-existence with Fh and OM in natural environments. Here Fh-OM complexes were synthesized in the presence of montmorillonite (SWy-2), forming ternary Fh-(SWy-2)-OM complexes. A metal-reducing bacterium Geobacter sulfurreducens was used to reduce Fh in the complexes under circumneutral pH and anoxic conditions with or without H 2 as extra electron donor. Various spectroscopy and mass spectrometry methods were used to monitor the progress of Fh bio-reduction and mineral/OM transformation. Results showed that G. sulfurreducens utilized mineral-bound OM as electron donor and/or carbon source to couple with Fh reduction. Relative to Fh-OM complex, Addition of SWy-2 to Fh-OM complex enhanced the bio-reduction extent of Fh by increasing the proportion of bioavailable OM that was weakly bound to SWy-2. However, its effect on the bio-reduction rate was variable. SWy-2 initially decreased the rate, because it spatially separated OM (electron donor) from Fh (electron acceptor). During later incubation, SWy-2 increased the reduction rate by sorbing biogenic Fe 2+ that would otherwise passivate the Fh and cell surfaces. Bio-reduction transformed mineral-bound OM to microbial products (e.g. necromass, extracellular polymeric substances), but organic compounds with aromatic structures, carboxyl groups and large molecular weight were more resistant to desorption and oxidation. The persistence of these compounds against bio-reduction induced transformation is likely due to their stronger binding with minerals and/or lower nominal oxidation states of carbon relative to other compounds. Our results provide new insights into the role of clay minerals in regulating biogeochemical cycling of solid-phase Fe and transformation of mineral-associated OM in anoxic soil environments.
58 GEOSCIENCES↗
Mechanisms of Enhanced Antibacterial Activity by Reduced Chitosan-Intercalated Nontronite
Previous studies have documented the antibacterial activity of certain iron-containing clays. However, the repulsion between negatively charged bacteria and the clay surface makes this process inefficient. The objective of this study is to improve the bactericidal efficiency of clays by reversing their surface charge from negative to positive. To achieve this objective, here positively charged chitosan, a nontoxic and biodegradable polymer, was intercalated into nontronite NAu-2. Chitosan-intercalated NAu-2 (C-NAu-2) was chemically reduced to obtain reduced C-NAu-2 (rC-NAu-2). Relative to reduced nontronite (rNAu-2), the antibacterial activity of rC-NAu-2 is higher and more persistent over a pH range of 6–8. The close spatial association between positively charged rC-NAu-2 and negatively charged bacteria increases the chances of cell membrane attack by extracellular ROS, the influx of soluble Fe 2+ into the bacterial cell, and the yield of intracellular ROS. All these factors contribute to the enhanced antibacterial activity of rC-NAu-2. In contrast to rNAu-2 treated E. coli cells, where membrane damage and intracellular ROS/Fe accumulation are restricted to the polar regions, the close bacteria–clay association in rC-NAu-2 results in nonselective membrane damage and more uniform intracellular ROS/Fe distribution across whole bacterial cells. These results advance the antibacterial model by highlighting the importance of bacteria–clay interactions to the antibacterial activity of Fe-bearing clays.
59 BASIC BIOLOGICAL SCIENCES↗
Chemical oxygen demand (COD) removal from bio-treated coking wastewater by hydroxyl radicals produced from a reduced clay mineral
Removal of chemical oxygen demand (COD) from wastewater has been of considerable interest for several decades, but detailed mechanisms are poorly known. Here we present an environmental friendly method for removing COD from coking wastewater by using chemically reduced nontronite (rNAu-2). Hydroxyl radicals (·OH) produced from oxidation of structural Fe(II) in rNAu-2 in phosphate buffer at pH 6.5, oxidized various compounds in wastewater and thus significantly decreased COD (from 199.10 ± 0.90 to 80.4 ± 1.97 mg/L) within 120 h. The amount of COD removal was positively correlated with the amount of ·OH production, with removal efficiency depending on pH and buffer type. Mass spectrometric analysis of dissolved organic matter (DOM) suggested an oxidative pathway for COD removal. Excitation-emission matrix (EEM) fluorescence spectroscopy showed that aromatic protein-like compounds accounted for a large fraction of DOM in initial wastewater, but after rNAu-2 treatment, their proportion decreased. A sequential treatment of wastewater by rNAu-2 and a common wastewater bacterium Alcaligenes faecalis demonstrated that different orders of chemical and biological treatments affected COD removal efficiency, likely because chemical and microbial treatments targeted different compounds in coking wastewater.
Zhou, Ziqi↗