Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions

BACKGROUND: The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. METHODOLOGY/PRINCIPAL FINDINGS: The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR (31)P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The (31)P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. CONCLUSIONS/SIGNIFICANCE: The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions

Fuzzy multi-objective optimization case study based on an anaerobic co-digestion process of food waste leachate and piggery wastewater

This paper presents the development and evaluation of fuzzy multi-objective optimization for decision-making that includes the process optimization of anaerobic digestion (AD) process. The operating cost criteria which is a fundamental research gap in previous AD analysis was integrated for the case study in this research. In this study, the mixing ratio of food waste leachate (FWL) and piggery wastewater (PWW), calcium carbonate (CaCO3) and sodium chloride (NaCl) concentrations were optimized to enhance methane production while minimizing operating cost. The results indicated a maximum of 63.3% satisfaction for both methane production and operating cost under the following optimal conditions: mixing ratio (FWL: PWW) – 1.4, CaCO3 – 2970.5 mg/L and NaCl – 2.7 g/L. In multi-objective optimization, the specific methane yield (SMY) was 239.0 mL CH4/g VSadded, while 41.2% volatile solids reduction (VSR) was obtained at an operating cost of 56.9 US$/ton. In comparison with the previous optimization study that utilized the response surface methodology, the SMY, VSR and operating cost of the AD process were 310 mL/g, 54$/ton, respectively. The results from multi-objective fuzzy optimization proves to show the potential application of this technique for practical decision-making in the process optimization of AD process. © 2018 Elsevier Lt

Solidification/stabilization of ASR fly ash using thiomer material: Optimization of compressive strength and heavy metals leaching

Optimization studies of a novel and eco-friendly construction material, Thiomer, was investigated in the solidification/stabilization of automobile shredded residue (ASR) fly ash. A D-optimal mixture design was used to evaluate and optimize maximum compressive strength and heavy metals leaching by varying Thiomer (20–40 wt%), ASR fly ash (30–50 wt%) and sand (20–40 wt%). The analysis of variance was utilized to determine the level of significance of each process parameters and interactions. The microstructure of the solidified materials was taken from a field emission-scanning electron microscopy and energy dispersive X-ray spectroscopy that confirmed successful Thiomer solidified ASR fly ash due to reduced pores and gaps in comparison with an untreated ASR fly ash. The X-ray diffraction detected the enclosed materials on the ASR fly ash primarily contained sulfur associated crystalline complexes. Results indicated the optimal conditions of 30 wt% Thiomer, 30 wt% ASR fly ash and 40 wt% sand reached a compressive strength of 54.9 MPa. For the optimum results in heavy metals leaching, 0.0078 mg/L Pb, 0.0260 mg/L Cr, 0.0007 mg/L Cd, 0.0020 mg/L Cu, 0.1027 mg/L Fe, 0.0046 mg/L Ni and 0.0920 mg/L Zn were leached out, being environmentally safe due to being substantially lower than the Korean standard leaching requirements. The results also showed that Thiomer has superiority over the commonly used Portland cement as a binding material which confirmed its potential usage as an innovative approach to simultaneously synthesize durable concrete and satisfactorily pass strict environmental regulations by heavy metals leaching. © 2017 Elsevier Lt

Thiomer solidification of an ASR bottom ash: Optimization based on compressive strength and the characterization of heavy metal leaching

This study examines the function of Thiomer solidification as a novel environment friendly construction material and its immobilization capacity over heavy metals in the automotive shredder residue (ASR) bottom ash. The morphology of the mixture using a field emission-scanning electron microscopy consistently illustrated the effective bonding between Thiomer and sand towards ASR bottom ash due to acting as fillers to reduce the gaps in its surface during Thiomer solidification. A D-optimal mixture design was further utilized in order to evaluate and optimize the parameters of Thiomer (25–35 wt%), ASR bottom ash (30–45 wt%) and sand (30–40 wt%) on the response of compressive strength. Result showed that optimum compressive strength of 55.9 MPa can be attained at 33.6, 36.4 and 30.0 wt% of Thiomer, ASR bottom ash and sand, respectively. The solidified Thiomer specimen showed superior structural strength over ordinary Portland cement concrete at curing time of 1 and 7 days. Furthermore, a mean heavy metal concentrations of 0.055 ppm Cu2+, 0.105 ppm Zn2+, 0.045 ppm Pb2+, 0.078 ppm Cr6+ and 0.002 ppm Cd2+ were achieved at various mixture designs in the heavy metal immobilization which satisfies stringent environmental standards. Thus, the application of Thiomer proves to be a promising construction material that can pose as an alternative over common cement due to promoting high durability and being eco-friendly. © 2017 Elsevier Lt

Co-benefit potential of industrial and urban symbiosis using waste heat from industrial park in Ulsan, Korea

© 2017 Energy depletion and global climate change have stimulated the Korean government to strengthen energy saving and efficiency measures in all sectors. However, in industrial sector where huge energy is consumed, only small portions of the high-grade waste heat from industrial processes have been utilized by another process through industrial symbiosis networks in industrial park and large quantities of low-grade waste heat are mostly discharged into the environment. Through technological assessment of energy balance between waste heat source in industrial park and heat sink in industrial park and urban area, this study systematically develops an industrial-urban symbiosis (I-US) and conducts a co-benefit analysis for 4 scenarios. Based on the investigation on the energy utilization status of Ulsan, the scenarios for potential I-US networks are evaluated. For the supply and demand side, potential energy sources and sinks are estimated at 49,321 and 15,424 TJ/yr, respectively, noting that the demand side considered four scenarios based on the local condition analysis. Through these scenarios for the energy symbiosis networks; a reduction of 243,396 ton/yr CO2 emission and 48 million US Dollar/yr fuel cost were achieved. Due to a large transition cost for a district heating system, I-US public private partnership business model is highly recommended to attract long-term investment and institutional incentives of carbon credit and energy service companies fund are conducive to put these scenarios into practice

Improvement of Switching Speed of a 600-V Nonpunch-Through Insulated Gate Bipolar Transistor Using Fast Neutron Irradiation

Fast neutron irradiation was used to improve the switching speed of a 600-V nonpunch-through insulated gate bipolar transistor. Fast neutron irradiation was carried out at 30-MeV energy in doses of 1 × 108 n/cm2, 1 × 109 n/cm2, 1 × 1010 n/cm2, and 1 × 1011 n/cm2. Electrical characteristics such as current–voltage, forward on-state voltage drop, and switching speed of the device were analyzed and compared with those prior to irradiation. The on-state voltage drop of the initial devices prior to irradiation was 2.08 V, which increased to 2.10 V, 2.20 V, 2.3 V, and 2.4 V, respectively, depending on the irradiation dose. This effect arises because of the lattice defects generated by the fast neutrons. In particular, the turnoff delay time was reduced to 92 nanoseconds, 45% of that prior to irradiation, which means there is a substantial improvement in the switching speed of the device