Genome-scale reconstruction of Salinispora tropica metabolism; Microbial engineering and its applications in secondary metabolite production

Bacteria within the order Actinomycetales are a well-known source of natural products such as antibiotics and anticancer agents, and the genus Salinispora is no exception. Salinispora tropica is a marine actinomycete that produces diverse secondary metabolites, including many that possess pharmaceutical properties such as Salinosporamide A (NPI-0052), a potent anticancer agent, and sporolides, candidates for antiviral compounds. Here, we present the first manually curated genome-scale metabolic model (iCC908) for Salinispora tropica strain CNB-440. The reconstruction enables characterization of the metabolic capabilities for understanding and modeling the cellular physiology of this newly sequenced genome. The model was based on physiological and biochemical information of primary and secondary metabolism pathways. The reconstructed stoichiometric matrix consists of 1169 biochemical reactions, 204 transport reactions and 1317 metabolites. A total of 908 structural open reading frames (ORFs) were included in the reconstructed network. The number of gene functions included corresponds to 20% of all characterized ORFs in the S. tropica genome. The genome-scale metabolic model was used to study strain-specific capabilities in defined minimal media and to analyze growth capabilities in 41 different minimal growth-supporting environments. These nutrient sources were evaluated experimentally to assess the accuracy of in-silico growth simulations. The model predicted no auxotrophies for essential amino acids, which was corroborated experimentally. The strain is able to use 21 different carbon sources, 8 nitrogen sources and 4 sulfur sources from the nutrient sources tested. Cases where the model was incorrect provided opportunities to gain new insights into the physiology of this specie and generate hypotheses. The incorporation of modifications led to increased accuracy in predicting the outcome of growth/no growth experiments from 76 to 93%. New data, and modifications can be incorporated into the reconstruction to iteratively improve the reconstruction. Since specialized pathways were included in the reconstruction, growth simulations and in silico gene deletions can be performed by using flux balance analysis (FBA) to dramatically increase secondary metabolites production and yield in Salinispora for possible “gene cluster identification” so specific pathways can be cloned in more efficient strains. For example, iCC908 has been used to define a production medium to improve Salinosporamide A production in a recombinant strain with increases over 20% compared to the wild type. This presentation will describe the main features of the metabolic flux analysis and microbial engineering methodology based on reconstruction of the whole metabolism and its applications in the optimization of secondary metabolite production

Describing whisker morphology of the Carnivora

One of the largest ecological transitions in carnivoran evolution was the shift from terrestrial to aquatic lifestyles, which has driven morphological diversity in skulls and other skeletal structures. In this paper we investigate the association between those lifestyles and whisker morphology. However, comparing whisker morphology over a range of species is challenging since the number of whiskers and their positions on the mystacial pads vary between species. Also, each whisker will be at a different stage of growth and may have incurred damage due to wear and tear. Identifying a way to easily capture whisker morphology in a small number of whisker samples would be beneficial. Here, we describe individual and species variation in whisker morphology from two-dimensional scans in red fox, European otter and grey seal. A comparison of long, caudal whiskers shows interspecies differences most clearly. We go on to describe global whisker shape in 24 species of carnivorans, using linear approximations of curvature and taper, as well as traditional morphometric methods. We also qualitatively examine surface texture, or the presence of scales, using Scanning Electron Microscope images. We show that gross highly conserved, with whisker curvature and taper obeying simple linear relationships with length. However, measures of whisker base radius, length, and maybe even curvature, can vary between species and substrate preferences. Specifically, the aquatic species in our sample have thicker, shorter whiskers that are smoother, with less scales present than those of terrestrial species. We suggest that these thicker whiskers may be stiffer and able to maintain their shape and position during underwater sensing, but being stiffer may also increase wear

Nonlinear waves in a cylindrical Bose-Einstein condensate

We present a complete calculation of solitary waves propagating in a steady state with constant velocity v along a cigar-shaped Bose-Einstein trap approximated as infinitely-long cylindrical. For sufficiently weak couplings (densities) the main features of the calculated solitons could be captured by effective one-dimensional (1D) models. However, for stronger couplings of practical interest, the relevant solitary waves are found to be hybrids of quasi-1D solitons and 3D vortex rings. An interesting hierarchy of vortex rings occurs as the effective coupling constant is increased through a sequence of critical values. The energy-momentum dispersion of the above structures is shown to exhibit characteristics similar to a mode proposed sometime ago by Lieb within a strictly 1D model, as well as some rotonlike features.Comment: 10 pages, 12 figure

Herbicide-use trends in prairie canola production systems

Non-Peer Reviewe

Advance telephone calls ahead of reminder questionnaires increase response rate in non-responders compared to questionnaire reminders only : The RECORD phone trial

Peer reviewedPublisher PD

Noncolliding Squared Bessel Processes

We consider a particle system of the squared Bessel processes with index $\nu > -1$ conditioned never to collide with each other, in which if $-1 < \nu < 0$ the origin is assumed to be reflecting. When the number of particles is finite, we prove for any fixed initial configuration that this noncolliding diffusion process is determinantal in the sense that any multitime correlation function is given by a determinant with a continuous kernel called the correlation kernel. When the number of particles is infinite, we give sufficient conditions for initial configurations so that the system is well defined. There the process with an infinite number of particles is determinantal and the correlation kernel is expressed using an entire function represented by the Weierstrass canonical product, whose zeros on the positive part of the real axis are given by the particle-positions in the initial configuration. From the class of infinite-particle initial configurations satisfying our conditions, we report one example in detail, which is a fixed configuration such that every point of the square of positive zero of the Bessel function $J_{\nu}$ is occupied by one particle. The process starting from this initial configuration shows a relaxation phenomenon converging to the stationary process, which is determinantal with the extended Bessel kernel, in the long-term limit.Comment: v3: LaTeX2e, 26 pages, no figure, corrections made for publication in J. Stat. Phy

Mean-field analysis of collapsing and exploding Bose-Einstein condensates

The dynamics of collapsing and exploding trapped Bose-Einstein condensat es caused by a sudden switch of interactions from repulsive to attractive a re studied by numerically integrating the Gross-Pitaevskii equation with atomic loss for an axially symmetric trap. We investigate the decay rate of condensates and the phenomena of bursts and jets of atoms, and compare our results with those of the experiments performed by E. A. Donley {\it et al.} [Nature {\bf 412}, 295 (2001)]. Our study suggests that the condensate decay and the burst production is due to local intermittent implosions in the condensate, and that atomic clouds of bursts and jets are coherent. We also predict nonlinear pattern formation caused by the density instability of attractive condensates.Comment: 7 pages, 8 figures, axi-symmetric results are adde

Simple method for excitation of a Bose-Einstein condensate

An appropriate, time-dependent modification of the trapping potential may be sufficient to create effectively collective excitations in a cold atom Bose-Einstein condensate. The proposed method is complementary to earlier suggestions and should allow the creation of both dark solitons and vortices.Comment: 8 pages, 7 figures, version accepted for publication in Phys. Rev.

Cold sintering of bioglass and bioglass/polymer composites

Bioactive glasses are widely utilized to regenerate bone tissue and aid bonding of orthopedic implants. Forming composites of bioglass with bioactive polymers allow the mechanical properties and biological response to be tailored. Although several methods for creating bioglass–polymer composites exist, they require dissolution of the polymer, controlled phase separation, and appear to have an upper limit of ∼30 vol.% bioglass. Cold sintering is a novel technique for the densification of ceramics and glasses which utilizes a liquid phase and pressure to allow the production of components at reduced temperatures. We demonstrate that cold sintering (100°C) of Bioglass 45S5 powder produced via flame spray pyrolysis and the fabrication of Bioglass 45S5–polymer composites. Assessment of the in vitro response revealed that composites were not cytotoxic. Solid-state 31P and 29Si MAS NMR studies of the silicon and phosphorus speciation in the glass powder, as-received, wetted, and sintered samples show similarities to reactions expected when bioglass is implanted in the body which along with Raman spectroscopy data gave insight into the cold sintering densification mechanism

Infinite systems of non-colliding generalized meanders and Riemann-Liouville differintegrals

Yor's generalized meander is a temporally inhomogeneous modification of the $2(\nu+1)$-dimensional Bessel process with $\nu > -1$, in which the inhomogeneity is indexed by $\kappa \in [0, 2(\nu+1))$. We introduce the non-colliding particle systems of the generalized meanders and prove that they are the Pfaffian processes, in the sense that any multitime correlation function is given by a Pfaffian. In the infinite particle limit, we show that the elements of matrix kernels of the obtained infinite Pfaffian processes are generally expressed by the Riemann-Liouville differintegrals of functions comprising the Bessel functions $J_{\nu}$ used in the fractional calculus, where orders of differintegration are determined by $\nu-\kappa$. As special cases of the two parameters $(\nu, \kappa)$, the present infinite systems include the quaternion determinantal processes studied by Forrester, Nagao and Honner and by Nagao, which exhibit the temporal transitions between the universality classes of random matrix theory.Comment: LaTeX, 35 pages, v3: The argument given in Section 3.2 was simplified. Minor corrections were mad