THE CONTROL BY PHYTOCHROME OF NITRATE REDUCTASE IN THE CURD OF LIGHT-GROWN CAULIFLOWER

Abstract— The activity of nitrate reductase from the curd of light-grown cauliflower ( Brassica oleracea (L) var botrytis (DC) 'St. Hilary') is modulated by nitrate and by light. Using broad-band sources of equal photosynthetically active radiation but with different proportions of red and far-red light, a linear relationship between nitrate reductase activity and ψ(Estimated phytochrome photoequilibrium) was obtained. This relationship, apparent after 8 h incubation, was maintained and little altered after 48 h incubation. The linearity was apparent between ψE 0.26 and ψE 0.69; ψE 0.26 being no more effective than a dark control. Far-red reversibility confirmed the involvement of phytochrome. Brief pulses of red light were also used to establish a range of phytochrome photoequilibria within the tissue. Again a linear relationship between ψ and nitrate reductase activity was obtained with a threshold for the response at ψ 0.3. With both monochromatic and broad-band sources it was seen that neither photon fluence rate nor duration of exposure affected the final activity of the enzyme and that phytochrome was acting solely through ψ (or [Pfr] since phytochrome is stable in this tissue) to bring about these responses.     

Insights into the Structure and Energy of DNA Nanoassemblies

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.     

PHOTOTROPISM AND AXIS EXTENSION IN LIGHT-GROWN MUSTARD (Sinapis alba L.) SEEDLINGS‡

Abstract— The relationship between phototropism and axis extension was examined in light-grown mustard (Sinapis alba L.) seedlings using the low pressure sodium lamp (SOX)? technique to eliminate growth responses due to phytochrome. Addition of blue light caused no net inhibition of hypocotyl elongation, but plants showed a phototropic response. Curvature was caused by a simultaneous inhibition of growth on the illuminated side of the hypocotyl and an acceleration on the shaded side. Phototropism thus occurs independently of axis elongation and suggests that they are two separate processes. The results are inconsistent with the Blaauw theory of phototropism.     

Dynamic criticality in glass-forming liquids

We propose that the dynamics of supercooled liquids and the formation of glasses can be understood from the existence of a zero-temperature dynamical critical point. To support our proposal, we derive a dynamic field theory for a generic kinetically constrained model, which we expect to describe the dynamics of a supercooled liquid. We study this field theory using the renormalization group (RG). Its long time behavior is dominated by a zero-temperature critical point, which for d>2 belongs to the directed percolation universality class. Molecular dynamics simulations seem to confirm the existence of dynamic scaling behavior consistent with the RG predictions.     

Development and use of an atomistic CHARMM‐based forcefield for peptoid simulation

Peptoids are positional isomers of peptides: peptoid sidechains are attached to backbone nitrogens rather than α‐carbons. Peptoids constitute a class of sequence‐specific polymers resistant to biological degradation and potentially as diverse, structurally and functionally, as proteins. While molecular simulation of proteins is commonplace, relatively few tools are available for peptoid simulation. Here, we present a first‐generation atomistic forcefield for peptoids. Our forcefield is based on the peptide forcefield CHARMM22, with key parameters tuned to match both experimental data and quantum mechanical calculations for two model peptoids (dimethylacetamide and a sarcosine dipeptoid). We used this forcefield to demonstrate that solvation of a dipeptoid substantially modifies the conformations it can access. We also simulated a crystal structure of a peptoid homotrimer, H‐(N‐2‐phenylethyl glycine)₃‐OH, and we show that experimentally observed structural and dynamical features of the crystal are accurately described by our forcefield. The forcefield presented here provides a starting point for future development of peptoid‐specific simulation methods within CHARMM. © 2013 Wiley Periodicals, Inc.     

PHOTORESPONSES OF Arabidopsis SEEDLINGS EXPRESSING AN INTRODUCED OAT phyA cDNA: PERSISTENCE OF ETIOLATED PLANT TYPE RESPONSES IN LIGHT-GROWN PLANTS

The photocontrol of hypocotyl elongation has been studied in etiolated and light-grown wild type (WT) Arabidopsis thaliana (L. Heynh) seedlings, and in two homozygous isogenic lines that have been transformed with the oat phy A gene coding sequence under the control of the cauliflower mosaic virus (CaMV) 35S promoter. For etiolated seedlings the inhibition of hypocotyl elongation by continuous broad band far-red light (FR) is saturated at much lower photon fluence rates in the transgenic seedlings compared with WT seedlings. Furthermore, whereas de-etiolation of WT seedlings leads to loss of responsiveness of the hypocotyls to prolonged FR, de-etiolated transgenic seedlings continue to show a pronounced FR-mediated inhibition of elongation. This may reflect the persistence of a FR-high irradiance response (HIR) mediated by the introduced oat phytochrome A. Although the hypocotyls of light-grown transgenic seedlings display a qualitatively normal end-of-day FR growth promotion, such seedlings display an aberrant shade-avoidance response to reduced red:far-red ratio (R:FR). These results are discussed in relation to the proposal that the constitutive expression of phytochrome A leads to the persistence of photoresponse modes normally restricted to etiolated plants.     

Design Rules for Self‐Assembly of 2D Nanocrystal/Metal–Organic Framework Superstructures

We demonstrate the guiding principles behind simple two dimensional self‐assembly of MOF nanoparticles (NPs) and oleic acid capped iron oxide (Fe₃O₄) NCs into a uniform two‐dimensional bi‐layered superstructure. This self‐assembly process can be controlled by the energy of ligand–ligand interactions between surface ligands on Fe₃O₄ NCs and Zr₆O₄(OH)₄(fumarate)₆ MOF NPs. Scanning transmission electron microscopy (TEM)/energy‐dispersive X‐ray spectroscopy and TEM tomography confirm the hierarchical co‐assembly of Fe₃O₄ NCs with MOF NPs as ligand energies are manipulated to promote facile diffusion of the smaller NCs. First‐principles calculations and event‐driven molecular dynamics simulations indicate that the observed patterns are dictated by combination of ligand–surface and ligand–ligand interactions. This study opens a new avenue for design and self‐assembly of MOFs and NCs into high surface area assemblies, mimicking the structure of supported catalyst architectures, and provides a thorough fundamental understanding of the self‐assembly process, which could be a guide for designing functional materials with desired structure.     

Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles

We introduce a "virtual-move" Monte Carlo algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an important realization being self-assembling particles endowed with strong, short-ranged, and angularly specific ("patchy") attractions. Standard Monte Carlo techniques employ sequential updates of particles and can suffer from low acceptance rates when attractions are strong. In this event, collective motion can be strongly suppressed. Our algorithm avoids this problem by proposing simultaneous moves of collections (clusters) of particles according to gradients of interaction energies. One particle first executes a "virtual" trial move. We determine which of its neighbors move in a similar fashion by calculating individual bond energies before and after the proposed move. We iterate this procedure and update simultaneously the positions of all affected particles. Particles move according to an approximation of realistic dynamics without requiring the explicit computation of forces and without the step size restrictions required when integrating equations of motion. We employ a size- and shape-dependent damping of cluster movements, motivated by collective hydrodynamic effects neglected in simple implementations of Brownian dynamics. We discuss the virtual-move algorithm in the context of other Monte Carlo cluster-move schemes and demonstrate its utility by applying it to a model of biological self-assembly.     

Electrostatics and aggregation: how charge can turn a crystal into a gel

The crystallization of proteins or colloids is often hindered by the appearance of aggregates of low fractal dimension called gels. Here we study the effect of electrostatics upon crystal and gel formation using an analytic model of hard spheres bearing point charges and short range attractive interactions. We find that the chief electrostatic free energy cost of forming assemblies comes from the entropic loss of counterions that render assemblies charge-neutral. Because there exists more accessible volume for these counterions around an open gel than a dense crystal, there exists an electrostatic entropic driving force favoring the gel over the crystal. This driving force increases with increasing sphere charge, but can be counteracted by increasing counterion concentration. We show that these effects cannot be fully captured by pairwise-additive macroion interactions of the kind often used in simulations, and we show where on the phase diagram to go in order to suppress gel formation.