A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli

Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB)

Fractional Klein-Kramers equation for superdiffusive transport: normal versus anomalous time evolution in a differential L{\'e}vy walk model

We introduce a fractional Klein-Kramers equation which describes sub-ballistic superdiffusion in phase space in the presence of a space-dependent external force field. This equation defines the differential L{\'e}vy walk model whose solution is shown to be non-negative. In the velocity coordinate, the probability density relaxes in Mittag-Leffler fashion towards the Maxwell distribution whereas in the space coordinate, no stationary solution exists and the temporal evolution of moments exhibits a competition between Brownian and anomalous contributions.Comment: 4 pages, REVTe

Occurrence of periodic Lam\'e functions at bifurcations in chaotic Hamiltonian systems

We investigate cascades of isochronous pitchfork bifurcations of straight-line librating orbits in some two-dimensional Hamiltonian systems with mixed phase space. We show that the new bifurcated orbits, which are responsible for the onset of chaos, are given analytically by the periodic solutions of the Lam\'e equation as classified in 1940 by Ince. In Hamiltonians with C_${2v}$ symmetry, they occur alternatingly as Lam\'e functions of period 2K and 4K, respectively, where 4K is the period of the Jacobi elliptic function appearing in the Lam\'e equation. We also show that the two pairs of orbits created at period-doubling bifurcations of touch-and-go type are given by two different linear combinations of algebraic Lam\'e functions with period 8K.Comment: LaTeX2e, 22 pages, 14 figures. Version 3: final form of paper, accepted by J. Phys. A. Changes in Table 2; new reference [25]; name of bifurcations "touch-and-go" replaced by "island-chain

Calculation of atomic spontaneous emission rate in 1D finite photonic crystal with defects

We derive the expression for spontaneous emission rate in finite one-dimensional photonic crystal with arbitrary defects using the effective resonator model to describe electromagnetic field distributions in the structure. We obtain explicit formulas for contributions of different types of modes, i.e. radiation, substrate and guided modes. Formal calculations are illustrated with a few numerical examples, which demonstrate that the application of effective resonator model simplifies interpretation of results.Comment: Cent. Eur. J. Phys, in pres

Facile access to a heterocyclic, sp3-rich chemical scaffold via a tandem condensation/intramolecular nitrone–alkene [3+2] cycloaddition strategy

A heterocyclic, sp3-rich chemical scaffold was synthesised in just 6 steps via a highly regio- and diastereo-selective tandem nitrone formation/intramolecular nitrone–alkene [3+2] cycloaddition reaction. A library of 543 lead-like compounds based on the scaffold core has been produced

Memory-encoding vibrations in a disconnecting air bubble

Many nonlinear processes, such as the propagation of waves over an ocean or the transmission of light pulses down an optical fibre1, are integrable in the sense that the dynamics has as many conserved quantities as there are independent variables. The result is a time evolution that retains a complete memory of the initial state. In contrast, the nonlinear dynamics near a finite-time singularity, in which physical quantities such as pressure or velocity diverge at a point in time, is believed to evolve towards a universal form, one independent of the initial state2. The break-up of a water drop in air3 or a viscous liquid inside an immiscible oil4,5 are processes that conform to this second scenario. These opposing scenarios collide in the nonlinearity produced by the formation of a finite-time singularity that is also integrable. We demonstrate here that the result is a novel dynamics with a dual character

Specialized ommatidia of the polarization-sensitive dorsal rim area in the eye of monarch butterflies have non-functional reflecting tapeta

Many insects exploit sky light polarization for navigation or cruising-course control. The detection of polarized sky light is mediated by the ommatidia of a small specialized part of the compound eye: the dorsal rim area (DRA). We describe the morphology and fine structure of the DRA in monarch butterflies (Danaus plexippus). The DRA consists of approximately 100 ommatidia forming a narrow ribbon along the dorsal eye margin. Each ommatidium contains two types of photoreceptor with mutually orthogonal microvilli orientations occurring in a 2:6 ratio. Within each rhabdomere, the microvilli are well aligned. Rhabdom structure and orientation remain constant at all retinal levels, but the rhabdom profiles, as seen in tangential sections through the DRA, change their orientations in a fan-like fashion from the frontal to the caudal end of the DRA. Whereas these properties (two microvillar orientations per rhabdom, microvillar alignment along rhabdomeres, ommatidial fan array) are typical for insect DRAs in general, we also report and discuss here a novel feature. The ommatidia of monarch butterflies are equipped with reflecting tapeta, which are directly connected to the proximal ends of the rhabdoms. Although tapeta are also present in the DRA, they are separated from the rhabdoms by a space of approximately 55 μm effectively inactivating them. This reduces self-screening effects, keeping polarization sensitivity of all photoreceptors of the DRA ommatidia both high and approximately equal

Order and Stochastic Dynamics in Drosophila Planar Cell Polarity

Cells in the wing blade of Drosophila melanogaster exhibit an in-plane polarization causing distal orientation of hairs. Establishment of the Planar Cell Polarity (PCP) involves intercellular interactions as well as a global orienting signal. Many of the genetic and molecular components underlying this process have been experimentally identified and a recently advanced system-level model has suggested that the observed mutant phenotypes can be understood in terms of intercellular interactions involving asymmetric localization of membrane bound proteins. Among key open questions in understanding the emergence of ordered polarization is the effect of stochasticity and the role of the global orienting signal. These issues relate closely to our understanding of ferromagnetism in physical systems. Here we pursue this analogy to understand the emergence of PCP order. To this end we develop a semi-phenomenological representation of the underlying molecular processes and define a “phase diagram” of the model which provides a global view of the dependence of the phenotype on parameters. We show that the dynamics of PCP has two regimes: rapid growth in the amplitude of local polarization followed by a slower process of alignment which progresses from small to large scales. We discuss the response of the tissue to various types of orienting signals and show that global PCP order can be achieved with a weak orienting signal provided that it acts during the early phase of the process. Finally we define and discuss some of the experimental predictions of the model

The shape of two-dimensional liquid bridges

We have studied a single vertical, two-dimensional liquid bridge spanning the gap between two flat, horizontal solid substrates of given wettabilities. For this simple geometry, the Young-Laplace equation can be solved (quasi-)analytically to yield the equilibrium bridge shape under gravity. We establish the range of gap widths (as described by a Bond number ${\rm Bo}$) for which the liquid bridge can exist, for given contact angles at the top and bottom substrates ($\theta_c^t$ and $\theta_c^b$, respectively). In particular, we find that the absolute maximum span of a liquid bridge is four capillary lengths, for $\theta_c^b=180^\circ$ and $\theta_c^t=0^\circ$; whereas for $\theta_c^b=0^\circ$ and $\theta_c^t=180^\circ$ no bridge can form, for any substrate separation. We also obtain the minimum value of the cross-sectional area of such a liquid bridge, as well as the conditions for the existence and positions of any necks or bulges and inflection points on its surface. This generalises our earlier work in which the gap was assumed to be spanned by a liquid film of zero thickness connecting two menisci at the bottom and top substrates

Clues to Neuro-Degeneration in Niemann-Pick Type C Disease from Global Gene Expression Profiling

BACKGROUND: Niemann-Pick Type C (NPC) disease is a neurodegenerative disease that is characterized by the accumulation of cholesterol and glycosphingolipids in the late endocytic pathway. The majority of NPC cases are due to mutations in the NPC1 gene. The precise function of this gene is not yet known. METHODOLOGY/PRINCIPAL FINDINGS: Using cDNA microarrays, we analyzed the genome-wide expression patterns of human fibroblasts homozygous for the I1061T NPC1 mutation that is characterized by a severe defect in the intracellular processing of low density lipoprotein-derived cholesterol. A distinct gene expression profile was identified in NPC fibroblasts from different individuals when compared with fibroblasts isolated from normal subjects. As expected, NPC1 mutant cells displayed an inappropriate homeostatic response to accumulated intracellular cholesterol. In addition, a number of striking parallels were observed between NPC disease and Alzheimer's disease. CONCLUSIONS/SIGNIFICANCE: Many genes involved in the trafficking and processing of amyloid precursor protein and the microtubule binding protein, tau, were more highly expressed. Numerous genes important for membrane traffic and the cellular regulation of calcium, metals and other ions were upregulated. Finally, NPC fibroblasts exhibited a gene expression profile indicative of oxidative stress. These changes are likely contributors to the pathophysiology of Niemann-Pick Type C disease