Thermodynamics of DNA binding and break repair by the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus

Klenow and Klentaq are the “large fragments” of the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus. Examination of the DNA binding thermodynamics of both polymerases to replication versus repair substrates shows that Klenow binds primed-template DNA with up to 50X higher affinity than it binds to a nicked DNA, gapped DNAs, DNA with blunt-end or a 3’ overhang, while Klentaq binds all of these DNAs similarly. The presence of 5’ or 3’ phosphates has slightly different effects on DNA binding by both polymerases. In contrast, both polymerases bind mismatched DNA tighter than matched DNA, suggesting that they may share a similar mechanism to identify mismatched DNA, despite the lack of proofreading ability in Klentaq. The effects of Klenow and Klentaq on ligation of DNA ligase were also studied. Both polymerases stimulate the intermolecular ligation activity of E. coli DNA ligase at concentrations sub-stoichiometric to the DNA concentration. This effect occurs with E. coli DNA ligase, but not for T4 and Taq ligases. Additionally, neither polymerase significantly enhances ligation of a substrate containing a single nick, suggesting that the polymerases bridge the two DNA ends during intermolecular ligation. The nucleotide incorporation activities of both polymerases on substrates minicing double-strand breaks (DSBs) were also examined. Both proteins are able to “repair” DSBs via alignment-based strand-displacement DNA synthesis. Moreover, their repair abilities have different dependences on 5’ phosphate and DNA ligase when DSBs contain non-cohesive ends. Additionally, both proteins mediated palindrome amplification alone when the short inverted repeats occur near DNA breaks, suggesting that short inverted repeats in prokaryotes may help in DSB repair. 5’ phosphate at the matched break end is required for DSBs repair by both polymerases when one break end contains 3 consecutive mismatches. Results of the electrophoretic mobility shift assay show that Klenow-DNA complexes are observed as slow or fast moving bands, or both while all Klentaq-DNA complexes are observed as slow moving bands. The protection of both ends of a DNA by Klenow from exonuclease digestion suggests that the slow moving bands may correspond to the 2:1 polymerase-DNA complex

Use of Wheat Distiller Grains in Ruminant Diets

Wheat grain is commonly used to produce ethanol in Canada and Europe. During ethanol production processing, starch in the grain is fermented almost completely, and the remaining protein, fibre, fat, minerals and vitamins increase approximately 3-fold in concentration compared to the original grain. By-product derived from the ethanol production is named distiller grain and primarily used in feeding livestock animals. Wheat-based distiller grain is high in energy, protein and fibre. These properties give wheat distiller grain unique feeding opportunities for various classes of livestock as both energy and protein supplements as well as fibre source. This chapter summarizes some recent research findings published in peer reviewed and extension chapter on the use of wheat distiller grain in ruminant diets. Substantial variation in chemical composition exists among the distiller grain samples, which are mainly influenced by inherent original grain and technology used in ethanol plant. Wheat distiller grain can be used to partly replace grain or forage portion at moderate levels to meet energy and fibre requirements of cattle. A manure management plan needs to be developed that considers the fact that inclusion of wheat distiller grain in the diet will dramatically increase the nitrogen and phosphorus content in manure

Pol I DNA polymerases stimulate DNA end-joining by Escherichia coli DNA ligase

© 2018 Klenow and Klentaq are the large fragment domains of the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus, respectively. Herein, we show that both polymerases can significantly stimulate complementary intermolecular end-joining ligations by E.coli DNA ligase when the polymerases are present at concentrations lower than that of the DNA substrates. In contrast, high polymerase concentrations relative to the DNA substrates inhibit the intermolecular ligation activity of DNA ligase. Neither polymerase was able to stimulate the DNA ligase from T4 bacteriophage. Additionally, nick-closure by E. coli DNA ligase (but not T4 ligase) is slightly stimulated by both polymerases, but only at about 10% of the magnitude seen for end-joining enhancement. The data represent one of the first observations of direct polymerase-ligase interactions in prokaryotes, and suggest that the polymerases stabilize the associated DNA ends during intermolecular ligation, and that such a complex can be taken advantage of by some, but not all, DNA ligases

Fabrication of super-hydrophobic nickel film on copper substrate with improved corrosion inhibition by electrodeposition process

Inspired by the famous “lotus effect”, we have fabricated the super-hydrophobic surfaces with nickel film on copper substrates using a one-step electrodeposition method. By adjusting processing time, water contact angle of as-prepared surfaces can reach as high as 160.3 ± 1.5° with small rolling angle of 3.0 ± 0.5°, showing excellent super-hydrophobicity. After the deposition of nickel coating, the pristine copper surfaces became much rough with packed cauliflower-/thorn-like clusters. This unique surface texture contributed to trapping large amount of air and forming the air cushion underneath the water droplet, which can prevent the liquids contacting the copper substrate. The examination of surface chemical compositions implied that the deposited super-hydrophobic coating consisted of nickel crystals and nickel myristate. In this research, the formation mechanism of the electrodeposited super-hydrophobicity was extensively explained based on the analyses of surface texture and surface chemistry. Moreover, the corrosion resistance of the as-fabricated super-hydrophobic surface was estimated by the potentiodynamic polarization tests as well as the electrochemical impedance spectroscopy (EIS) measurements. The results demonstrate that the super-hydrophobic nickel coating showed excellent corrosion inhibition in simulated seawater solution. The existence of the super-hydrophobic coating could be regarded as a barrier and thus provide a perfect air-liquid interface that inhibits the penetration of the corrosive ions. This facile and effective method of electrodeposition process offers a promising approach for mass production of super-hydrophobic surfaces on various metals

Insights into the wettability transition of nanosecond laser ablated surface under ambient air exposure

Super-hydrophobic surfaces are attractive due to self-cleaning and anti-corrosive behaviors in harsh environments. Laser texturing offers a facile method to produce super-hydrophobic surfaces. However, the results indicated that the fresh laser ablated surface was generally super-hydrophilic and then gradually reached super-hydrophobic state when exposed to ambient air for certain time. Investigating wettability changing mechanism could contribute to reducing wettability transition period and improving industrial productivity. To solve this problem, we have studied the bare aluminum surface, fresh laser ablated super-hydrophilic surface, 15-day air exposed surface, and the aged super-hydrophobic surface by time-dependent water contact angle (WCA) and rolling angle (RA), scanning electron microscopy (SEM), 3D profile and X-ray photoelectron spectroscopy (XPS). The origins of super-hydrophilicity of the fresh laser ablated surface are identified as (1) the formation of hierarchical rough structures and (2) the surface chemical modifications (the decrease of nonpolar carbon, the formation of hydrophilic alumina and residual unsaturated atoms). The chemisorbed nonpolar airborne hydrocarbons from air moisture contributed to the gradual super-hydrophobic transition, which can be proved by the thermal annealing experiment. Particularly, to clearly explore the wettability transition mechanism, we extensively discussed why the laser-induced freshly outer layer was super-hydrophilic and how the airborne hydrocarbons were chemisorbed. This work not only provides useful insights into the formation mechanism of laser ablated super-hydrophobic surfaces, but also further guides industry to effectively modify surface chemistry to reduce wettability transition period and rapidly produce stable and durable super-hydrophobic surfaces. [Abstract copyright: Copyright © 2018. Published by Elsevier Inc.

Modification of wetting property of Inconel 718 surface by nanosecond laser texturing

Topographic and wetting properties of Inconel 718 (IN718) surfaces were modified via nanosecond laser treatment. In order to investigate surface wetting behavior without additional post treatment, three kinds of microstructures were created on IN718 surfaces, including line pattern, grid pattern and spot pattern. From the viewpoint of surface morphology, the results show that laser ablated grooves and debris significantly altered the surface topography as well as surface roughness compared with the non-treated surfaces. The effect of laser parameters (such as laser scanning speed and laser average power) on surface features was also discussed. We have observed the treated surface of IN718 showed very high hydrophilicity just after laser treatment under ambient air condistion.And this hydrophicility property has changed rapidly to the other extreme; very high hydrophobicity over just about 20 days. Further experiments and analyses have been carried out in order to investigate this phenomena. Based on the XPS analysis, the results indicate that the change of wetting property from hydrophilic to hydrophobic over time is due to the surface chemistry modifications, especially carbon content. After the contact angles reached steady state, the maximum water contact angle (WCA) for line-patterned and grid-patterned surfaces increased to 152.3 1.2° and 156.8 1.1° with the corresponding rolling angle (RA) of 8.8 1.1° and 6.5 0.8°, respectively. These treated IN718 surfaces exhibited superhydrophobic property. However, the maximum WCA for the spot-patterned surfaces just increased to 140.8 2.8° with RA above 10°. Therefore, it is deduced that laser-inscribed modification of surface wettability has high sensitivity to surface morphology and surface chemical compositions. This work can be utilized to optimize the laser processing parameters so as to fabricate desired IN718 surfaces with hydrophobic or even superhydrophobic property and thus extend the applications of IN718 material in various fields

Lithography-induced hydrophobic surfaces of silicon wafers with excellent anisotropic wetting properties

In recent years, hydrophobic surfaces have attracted more and more attentions from many researchers. In this paper, we comprehensively discussed the effects of specific parameters of microstructures on the wetting properties by using the theoretical models, the effects of microstructures on two-dimensional anisotropic properties and the water droplet impact experiment. Firstly, the relationships between the CAs and variable parameters were explored after the formula derivation for three various patterns. Then three different patterns were fabricated successfully on the silicon wafers by lithography technology and the effects of microstructures (including LWD parameters and interval parameters) on surface wettability were studied based on the theoretical research. After that, the effects of microstructures on two-dimensional anisotropic properties were also studied. Finally, the water droplet impact experiment was carried out and the viscoelastic properties were simply investigated. Our research proposed a potential method for fabricating hydrophobic surfaces with excellent anisotropic properties. This method may be widely used in a variety of academic and industrial applications in the future