Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening

Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of virus technology to express genes to induce phenotypes or to complement mutants in order to understand the function of plant genes is not well documented. Here we exploit Potato virus X as a tool for virus-induced gene complementation (VIGC). Using VIGC in tomato, we demonstrated that ectopic viral expression of LeMADS-RIN, which encodes a MADS-box transcription factor (TF), resulted in functional complementation of the non-ripening rin mutant phenotype and caused fruits to ripen. Comparative gene expression analysis indicated that LeMADS-RIN up-regulated expression of the SBP-box (SQUAMOSA promoter binding protein-like) gene LeSPL-CNR, but down-regulated the expression of LeHB-1, an HD-Zip homeobox TF gene. Our data support the hypothesis that a transcriptional network may exist among key TFs in the modulation of fruit ripening in tomato

Flow-induced polymer separation through a nanopore: Effects of solvent quality

© 2017 The Royal Society of Chemistry. Using a hybrid simulation method that combines a lattice-Boltzmann approach for the flow and a molecular dynamics model for the polymer, we investigated the effect of solvent quality on the flow-induced polymer translocation through a nanopore. We demonstrate the nontrivial dependence of the translocation dynamics of polymers on the solvent quality, i.e., the enhancement in the polymer insolubility increases the critical velocity flux and shortens the translocation time. Accordingly, we propose a new strategy to separate polymers with different solubilities via their translocations in the nanopore by adjusting the velocity flux of the flow, which appears to be promising for the design of micro-scaled polymer separation devices

Effect of Bidispersity on Dynamics of Confined Polymer Films

Using Monte Carlo simulations, we studied the effect of bidispersity on the dynamics of polymer films capped between two neutral walls, where we chose three representative compositions for bidispersed polymer films. Our results demonstrate that the characteristic entanglement length is an important parameter to clarify the effect of the bidispersity on the dynamics of polymer films. For the short chains, shorter than the characteristic entanglement length, the average number of near-neighboring particles increases with the decrease of the film thickness and limits the diffusivity of the short chains, which is independent of the film compositions. However, the dynamics of the long chains, of which is above the characteristic entanglement length, is determined by the film’s composition. In our previous paper, we inferred from the structures and entanglements of the bidisperse system with short and long chains that the constraint release contributes significantly to the relaxation mechanism of long chains. By calculating the self-diffusion coefficient of long chains, we confirmed this prediction that, with a lower weight fraction of long chains, the self-diffusion coefficient of long chains decreases slowly with the decrease of the film thickness, which is similar to that of short chains. With a higher weight fraction of long chains, the competition between the disentanglement and the increased in the local degree of confinement which resulted in the self-diffusion coefficient of long chains varying non-monotonically with the film thickness. Furthermore, for the bidisperse system with long and long chains, the diffusivity of long chains was not affected by the constraint release, which varied nonmonotonically with the decrease of the film thickness due to the competition between the disentanglement and the enhanced confinement. Herein, compared with the previous work, we completely clarified the relationship between the structures and dynamics for three representative compositions of bidisperse polymer films, which contains all possible cases for bidisperse systems. Our work not only establishes a unified understanding of the dependency of dynamics on the bidispersity of polymer films, but also helps to understand the case of polydispersity, which can provide computational supports for various applications for polymer films

A Mechanistic Study of Asymmetric Transfer Hydrogenation of Imines on a Chiral Phosphoric Acid Derived Indium Metal-Organic Framework

A density functional theory (DFT) study is reported to examine the asymmetric transfer hydrogenation (ATH) of imines catalyzed by an indium metal-organic framework (In-MOF) derived from a chiral phosphoric acid (CPA). It is revealed that the imine and reducing agent (i.e., thiazoline) are simultaneously adsorbed on the CPA through H-bonding to form an intermediate, subsequently, a proton is transferred from thiazoline to imine. The transition state TS-R and TS-S are stabilized on the CPA via H-bonding. Compared to the TS-S, the TS-R has shorter H-bonding distances and longer C-H···π distances, it is more stable and experiences less steric hindrance. Consequently, the TS-R exhibits a lower activation barrier affording to the (R)-enantiomer within 68.1% ee in toluene. Imines with substituted groups such as −NO2, −F, and −OCH3 are used to investigate the substitution effects on the ATH. In the presence of an electron-withdrawing group like −NO2, the electrophilicity of imine is enhanced and the activation barrier is decreased. The non-covalent interactions and activation-strain model (ASM) analysis reveal that the structural distortions and the differential noncovalent interactions of TSs in a rigid In-MOF provide the inherent driving force for enantioselectivity. For −OCH3 substituted imine, the TS-S has the strongest steric hindrance, leading to the highest enantioselectivity. When the solvent is changed from toluene to dichloromethane, acetonitrile, and dimethylsulfoxide with increasing polarity, the activation energies of transition state increase whereas their difference decreases. This implies the reaction is slowed down and the enantioselectivity becomes lower in a solvent of smaller polarity. Among the four solvents, toluene turns out to be the best for the ATH. The calculated results in this study are in fairly good agreement with experimental observations. This study provides a mechanistic understanding of the reaction mechanism, as well as substitution and solvent effects on the activity and enantioselectivity of the ATH. The microscopic insights are useful for the development of new chiral MOFs toward important asymmetric reactions

Role of Chiral Skeleton in Chiral Phosphoric Acids Catalyzed Asymmetric Transfer Hydrogenation: A DFT Study

Chiral phosphoric acids (CPAs) have received considerable attention due to their high activity for enantioselective transformations. However, the role of various chiral skeletons of CPAs in regulating the mechanism and enantioselectivity of asymmetric transfer hydrogenation has remained unclear. Density functional theory (DFT) calculations are performed to elucidate the role of chiral skeletons on the acidity, mechanism, enantioselectivity, and kinetic stabilities of transition states (TSs) in Asymmetric Transfer Hydrogen (ATH) reaction catalyzed by five CPAs. We found that the acidity of CPAs is strongly dependent on the chiral skeleton. The origin of enantioselectivity of ATH reaction arises from the differential noncovalent interactions between TSs and CPAs. Moreover, the shape and size of the catalyst pocket depending on chiral skeletons play key roles in the stability of TSs and the enantioselectivity of ATH. This study might facilitate to design and computationally screening of CPAs and guide the strategic choice of CPA skeletons to reduce the experimental workload

Compositional redistribution and dynamic heterogeneity in mixed lipid membrane induced by polyelectrolyte adsorption: Effects of chain rigidity

Monte Carlo simulation is employed to investigate the interaction between a polyelectrolyte and a fluid mixed membrane containing neutral (phosphatidyl-choline, PC), monovalent anionic (phosphatidylserine, PS), and multivalent anionic (phosphatidylinositol, PIP2) lipids. The effects of the intrinsic polyelectrolyte rigidity and solution ionic strength on the lateral rearrangement and dynamics of different anionic lipid species are systematically studied. Our results show that, the increase of polyelectrolyte chain rigidity reduces the loss of polyelectrolyte conformational entropy and the energy gains in electrostatic interaction, but raises the demixing entropy loss of the segregated anionic lipids. Therefore, the polyelectrolyte/membrane adsorption strength exhibits a non-monotonic dependence on the polyelectrolyte rigid parameter k ang, and there exists a certain optimal k ang for which the adsorption strength is maximal. Because the less loss of chain conformational entropy dominates the increase of the demixing entropy loss of the segregated anionic lipids and the decreases of the electrostatic energy gains, the semiflexible polyelectrolyte adsorbs onto the membrane more firmly than the flexible one. Whereas, for the adsorption of rigid polyelectrolyte, larger anionic lipid demixing entropy loss and less energy gain in the electrostatic interaction dominate over the decrease of the polyelectrolyte conformation entropy loss, leading to the desorption of the chain from the membrane. By decreasing the ionic concentration of the salt solution, the certain optimal k ang shifts to larger values. The cooperative effects of the adsorbing polyelectrolyte beads determine the concentration gradients and hierarchical mobility of the bound anionic lipids, as well as the polyelectrolyte dynamics

Regulation of anionic lipids in binary membrane upon the adsorption of polyelectrolyte: A Monte Carlo simulation

We employ Monte Carlo simulations to investigate the interaction between an adsorbing linear flexible cationic polyelectrolyte and a binary fluid membrane. The membrane contains neutral phosphatidyl–choline, PC) and multivalent anionic (phosphatidylinositol, PIP2) lipids. We systematically study the influences of the solution ionic strength, the chain length and the bead charge density of the polyelectrolyte on the lateral rearrangement and the restricted mobility of the multivalent anionic lipids in the membrane. Our findings show that, the cooperativity effect and the electrostatic interaction of the polyelectrolyte beads can significantly affect the segregation extent and the concentration gradients of the PIP2 molecules, and further cooperate to induce the complicated hierarchical mobility behaviors of PIP2 molecules. In addition, when the polyelectrolyte brings a large amount of charges, it can form a robust electrostatic well to trap all PIP2 and results in local overcharge of the membrane. This work presents a mechanism to explain the membrane heterogeneity formation induced by the adsorption of charged macromolecule