Optimized system for plant regeneration of watermelon (Citrullus lanatus Thumb.)

The objective of this study was to establish an efficient and reproducible in vitro plant regeneration for Citrullus lanatus cv. Zaojia. To achieve optimal conditions for adventitious shoot induction, five explants (entire cotyledons, distal cotyledons, proximal cotyledons, cotyledonary node A and cotyledonary node B) were tested on MS medium supplemented with different concentrations and combinations of growth regulators (0 to 0.2 mg/L IAA and 1.0 to 5.0 mg/L BA), the results showed that entire cotyledons cultured in MS + BA (2.0mg/L) + IAA(0.2mg/L) achieved the highest regenerated rate (89.67%) and the optimal protocol screened in this experiment had 7.69 ± 0.10 shoots per explants. Adventitious shoots were able to elongate both on MS medium with 0.2 mg/L KT and 0.2 mg/L NAA; IBA 0.3mg/L was found to be effective in the production of root. Acclimatized plantlets transferred to pot resumed growth, and their stems and leaves elongated and expanded in one month.Key words: Watermelon (Citrullus lanatus Thumb.), optimized system, regeneration, cotyledon explants, cotyledonary node

Gated Diffusion-controlled Reactions

The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications

DNA nanostructure-based magnetic beads for potentiometric aptasensing

In this work, a simple, general, and sensitive potentiometric platform is presented, which allows potentiometric sensing to be applied to any class of molecule irrespective of the analyte charge. DNA nanostructures are self-assembled on magnetic beads via the incorporation of an aptamer into a hybridization chain reaction. The aptamer target binding event leads to the disassembly of the DNA nanostructures, which results in a dramatic change in the surface charge of the magnetic beads. Such a surface charge change can be sensitively detected by a polycation-sensitive membrane electrode using protamine as an indicator. With an endocrine disruptor bisphenol A as a model, the proposed potentiometric method shows a wide linear range from 0.1 to 100 nM with a low detection limit of 80 pM (3 sigma). The proposed sensing strategy will lay a foundation for the development of potentiometric sensors for highly sensitive and selective detection of various targets

Using electric current to surpass the microstructure breakup limit

The elongated droplets and grains can break up into smaller ones. This process is driven by the interfacial free energy minimization, which gives rise to a breakup limit. We demonstrated in this work that the breakup limit can be overpassed drastically by using electric current to interfere. Electric current free energy is dependent on the microstructure configuration. The breakup causes the electric current free energy to reduce in some cases. This compensates the increment of interfacial free energy during breaking up and enables the processing to achieve finer microstructure. With engineering practical electric current parameters, our calculation revealed a significant increment of the obtainable number of particles, showing electric current a powerful microstructure refinement technology. The calculation is validated by our experiments on the breakup of Fe3C-plates in Fe matrix. Furthermore, there is a parameter range that electric current can drive spherical particles to split into smaller ones

The Microscopic Origin of Residual Stress for Flat Self-Actuating Piezoelectric Cantilevers

In this study, flat piezoelectric microcantilevers were fabricated under low-stress Pb(Zr0.52Ti0.48)O3 (PZT) film conditions. They were analyzed using the Raman spectrum and wafer curvature methods. Based on the residual stress analysis, we found that a thickness of 1 μm was critical, since stress relaxation starts to occur at greater thicknesses, due to surface roughening. The (111) preferred orientation started to decrease when the film thickness was greater than 1 μm. The d33 value was closely related to the stress relaxation associated with the preferred orientation changes. We examined the harmonic response at different PZT cantilever lengths and obtained a 9.4-μm tip displacement at 3 Vp-p at 1 kHz. These analyses can provide a platform for the reliable operation of piezoelectric microdevices, potentially nanodevice when one needs to have simultaneous control of the residual stress and the piezoelectric properties

A Didactic Model of Macromolecular Crowding Effects on Protein Folding

A didactic model is presented to illustrate how the effect of macromolecular crowding on protein folding and association is modeled using current analytical theory and discrete molecular dynamics. While analytical treatments of crowding may consider the effect as a potential of average force acting to compress a polypeptide chain into a compact state, the use of simulations enables the presence of crowding reagents to be treated explicitly. Using an analytically solvable toy model for protein folding, an approximate statistical thermodynamic method is directly compared to simulation in order to gauge the effectiveness of current analytical crowding descriptions. Both methodologies are in quantitative agreement under most conditions, indication that both current theory and simulation methods are capable of recapitulating aspects of protein folding even by utilizing a simplistic protein model

Scoring docking conformations using predicted protein interfaces

BACKGROUND: Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). RESULTS: First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. CONCLUSION: Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations

Gate-tunable giant nonreciprocal charge transport in noncentrosymmetric oxide interfaces

A polar conductor, where inversion symmetry is broken, may exhibit directional propagation of itinerant electrons, i.e., the rightward and leftward currents differ from each other, when time-reversal symmetry is also broken. This potential rectification effect was shown to be very weak due to the fact that the kinetic energy is much higher than the energies associated with symmetry breaking, producing weak perturbations. Here we demonstrate the appearance of giant nonreciprocal charge transport in the conductive oxide interface, LaAlO3/SrTiO3, where the electrons are confined to two-dimensions with low Fermi energy. In addition, the Rashba spin???orbit interaction correlated with the sub-band hierarchy of this system enables a strongly tunable nonreciprocal response by applying a gate voltage. The observed behavior of directional response in LaAlO3/SrTiO3 is associated with comparable energy scales among kinetic energy, spin???orbit interaction, and magnetic field, which inspires a promising route to enhance nonreciprocal response and its functionalities in spin orbitronics

Epidermal Growth Factor Gene Polymorphism and Risk of Hepatocellular Carcinoma: A Meta-Analysis

BACKGROUND: Hepatocarcinogenesis is a complex process that may be influenced by many factors, including polymorphism in the epidermal growth factor (EGF) gene. Previous work suggests an association between the EGF 61*A/G polymorphism (rs4444903) and susceptibility to hepatocellular carcinoma (HCC), but the results have been inconsistent. Therefore, we performed a meta-analysis of several studies covering a large population to address this controversy. METHODS: PubMed, EMBASE, Google Scholar and the Chinese National Knowledge Infrastructure databases were systematically searched to identify relevant studies. Data were abstracted independently by two reviewers. A meta-analysis was performed to examine the association between EGF 61*A/G polymorphism and susceptibility to HCC. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. RESULTS: Eight studies were chosen in this meta-analysis, involving 1,304 HCC cases (1135 Chinese, 44 Caucasian and 125 mixed) and 2,613 controls (1638 Chinese, 77 Caucasian and 898 mixed). The EGF 61*G allele was significantly associated with increased risk of HCC based on allelic contrast (OR = 1.29, 95% CI = 1.16-1.44, p<0.001), homozygote comparison (OR = 1.79, 95% CI = 1.39-2.29, p<0.001) and a recessive genetic model (OR = 1.34, 95% CI = 1.16-1.54, p<0.001), while patients carrying the EGF 61*A/A genotype had significantly lower risk of HCC than those with the G/A or G/G genotype (A/A vs. G/A+G/G, OR = 0.66, 95% CI = 0.53-0.83, p<0.001). CONCLUSION: The 61*G polymorphism in EGF is a risk factor for hepatocarcinogenesis while the EGF 61*A allele is a protective factor. Further large and well-designed studies are needed to confirm this conclusion

In Silico Elucidation of the Recognition Dynamics of Ubiquitin

Elucidation of the mechanism of biomacromolecular recognition events has been a topic of intense interest over the past century. The inherent dynamic nature of both protein and ligand molecules along with the continuous reshaping of the energy landscape during the binding process renders it difficult to characterize this process at atomic detail. Here, we investigate the recognition dynamics of ubiquitin via microsecond all-atom molecular dynamics simulation providing both thermodynamic and kinetic information. The high-level of consistency found with respect to experimental NMR data lends support to the accuracy of the in silico representation of the conformational substates and their interconversions of free ubiquitin. Using an energy-based reweighting approach, the statistical distribution of conformational states of ubiquitin is monitored as a function of the distance between ubiquitin and its binding partner Hrs-UIM. It is found that extensive and dense sampling of conformational space afforded by the µs MD trajectory is essential for the elucidation of the binding mechanism as is Boltzmann sampling, overcoming inherent limitations of sparsely sampled empirical ensembles. The results reveal a population redistribution mechanism that takes effect when the ligand is at intermediate range of 1–2 nm from ubiquitin. This mechanism, which may be depicted as a superposition of the conformational selection and induced fit mechanisms, also applies to other binding partners of ubiquitin, such as the GGA3 GAT domain