A Combination of Metabolomics and Machine Learning Results in the Identification of a New Cyst Nematode Hatching Factor

Potato Cyst Nematodes (PCNs) are an economically important pest for potato growers. A crucial event in the life cycle of the nematode is hatching, after which the juvenile will move toward the host root and infect it. The hatching of PCNs is induced by known and unknown compounds in the root exudates of host plant species, called hatching factors (HFs, induce hatching independently), such as solanoeclepin A (solA), or hatching stimulants (HSs, enhance hatching activity of HFs). Unraveling the identity of unknown HSs and HFs and their natural variation is important for the selection of cultivars that produce low amounts of HFs and HSs, thus contributing to more sustainable agriculture. In this study, we used a new approach aimed at the identification of new HFs and HSs for PCNs in potato. Hereto, root exudates of a series of different potato cultivars were analyzed for their PCN hatch-inducing activity and their solA content. The exudates were also analyzed using untargeted metabolomics, and subsequently the data were integrated using machine learning, specifically random forest feature selection, and Pearson’s correlation testing. As expected, solA highly correlates with hatching. Furthermore, this resulted in the discovery of a number of metabolite features present in the root exudate that correlate with hatching and solA content, and one of these is a compound of m/z 526.18 that predicts hatching even better than solA with both data methods. This compound’s involvement in hatch stimulation was confirmed by the fractionation of three representative root exudates and hatching assays with the resulting fractions. Moreover, the compound shares mass fragmentation similarity with solA, and we therefore assume it has a similar structure. With this work, we show that potato likely produces a solA analogue, and we contribute to unraveling the hatch-inducing cocktail exuded by plant roots

WW--geometry of the Toda systems associated with non-exceptional simple Lie algebras

The present paper describes the $W$--geometry of the Abelian finite non-periodic (conformal) Toda systems associated with the $B,C$ and $D$ series of the simple Lie algebras endowed with the canonical gradation. The principal tool here is a generalization of the classical Pl\"ucker embedding of the $A$-case to the flag manifolds associated with the fundamental representations of $B_n$, $C_n$ and $D_n$, and a direct proof that the corresponding K\"ahler potentials satisfy the system of two--dimensional finite non-periodic (conformal) Toda equations. It is shown that the $W$--geometry of the type mentioned above coincide with the differential geometry of special holomorphic (W) surfaces in target spaces which are submanifolds (quadrics) of $CP^N$ with appropriate choices of $N$. In addition, these W-surfaces are defined to satisfy quadratic holomorphic differential conditions that ensure consistency of the generalized Pl\"ucker embedding. These conditions are automatically fulfiled when Toda equations hold.Comment: 30 pages, no figur

Regularization of point vortices for the Euler equation in dimension two

In this paper, we construct stationary classical solutions of the incompressible Euler equation approximating singular stationary solutions of this equation. This procedure is carried out by constructing solutions to the following elliptic problem [ -\ep^2 \Delta u=(u-q-\frac{\kappa}{2\pi}\ln\frac{1}{\ep})_+^p, \quad & x\in\Omega, u=0, \quad & x\in\partial\Omega, ] where $p>1$, $\Omega\subset\mathbb{R}^2$ is a bounded domain, $q$ is a harmonic function. We showed that if $\Omega$ is simply-connected smooth domain, then for any given non-degenerate critical point of Kirchhoff-Routh function $\mathcal{W}(x_1,...,x_m)$ with the same strength $\kappa>0$, there is a stationary classical solution approximating stationary $m$ points vortex solution of incompressible Euler equations with vorticity $m\kappa$. Existence and asymptotic behavior of single point non-vanishing vortex solutions were studied by D. Smets and J. Van Schaftingen (2010).Comment: 32page

Desingularization of vortices for the Euler equation

We study the existence of stationary classical solutions of the incompressible Euler equation in the plane that approximate singular stationnary solutions of this equation. The construction is performed by studying the asymptotics of equation -\eps^2 \Delta u^\eps=(u^\eps-q-\frac{\kappa}{2\pi} \log \frac{1}{\eps})_+^p with Dirichlet boundary conditions and $q$ a given function. We also study the desingularization of pairs of vortices by minimal energy nodal solutions and the desingularization of rotating vortices.Comment: 40 page

Advancing the taxonomy of economically important red seaweeds (Rhodophyta)

© 2017 British Phycological Society. The cultivation of red seaweeds for food (nori), agar and carrageenans is the basis of a valuable industry. However, taxonomic knowledge of these cultivated seaweeds and their wild relatives has not kept pace with advances in molecular systematics despite the fundamental importance of being able to identify commercially important species and strains, discover cryptic and endemic taxa and recognize non-native species with potentially damaging diseases and epiphytes. This review focuses on molecular taxonomic advances in the cultivated red algae with the highest commercial value globally: Eucheuma and Kappaphycus, Porphyra sensu lato and Gracilaria. All three groups are similarly taxonomically challenging: speciose, morphologically plastic, with poorly resolved species boundaries. Eucheuma and Kappaphycus are frequently misidentified and the molecular markers cox2-3 spacer, cox1 and RuBisCO spacer have helped in understanding phylogenetic relationships and identifying new species and haplotypes. In Porphyra sensu lato (Bangiales) species identification and phylogenetic relationships were highly problematic until a taxonomic revision based on a two-gene phylogeny (18S and rbcL) resulted in nine genera of bladed species. Pyropia, with at least 89 species, three in nori cultivation, has potential for new commercial evaluation. In Gracilaria sensu lato, earlier efforts to resolve species-level taxonomy and generic descriptions were superseded by application of molecular tools, including DNA sequences of the RuBisCO spacer, rbcL gene, 18S and the ITS region. Studies of these cultivated red algal genera highlight the need for a robust taxonomy, a more standardized approach to the molecular markers used and a comprehensive dataset for each representative species. Current work on DNA-based species delimitation, the emergence of high throughput sequencing, multi-gene phylogenies, publication of whole genomes (e.g. Porphyra umbilicalis) and genomes in the pipeline (e.g. Gracilaria) are increasingly improving our understanding of phylogenomic relationships and species relationships. This knowledge, in turn, can then be applied to improving red seaweed aquaculture

The Exact MSSM Spectrum from String Theory

We show the existence of realistic vacua in string theory whose observable sector has exactly the matter content of the MSSM. This is achieved by compactifying the E_8 x E_8 heterotic superstring on a smooth Calabi-Yau threefold with an SU(4) gauge instanton and a Z_3 x Z_3 Wilson line. Specifically, the observable sector is N=1 supersymmetric with gauge group SU(3)_C x SU(2)_L x U(1)_Y x U(1)_{B-L}, three families of quarks and leptons, each family with a right-handed neutrino, and one Higgs-Higgs conjugate pair. Importantly, there are no extra vector-like pairs and no exotic matter in the zero mode spectrum. There are, in addition, 6 geometric moduli and 13 gauge instanton moduli in the observable sector. The holomorphic SU(4) vector bundle of the observable sector is slope-stable.Comment: 15 pages, LaTeX; v2: Hidden sector is unstable, symbol typesetting error corrected, clarifications and references added; v3: New discussion of hidden secto

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

NMR Experiments on a Three-Dimensional Vibrofluidized Granular Medium

A three-dimensional granular system fluidized by vertical container vibrations was studied using pulsed field gradient (PFG) NMR coupled with one-dimensional magnetic resonance imaging (MRI). The system consisted of mustard seeds vibrated vertically at 50 Hz, and the number of layers N_ell <= 4 was sufficiently low to achieve a nearly time-independent granular fluid. Using NMR, the vertical profiles of density and granular temperature were directly measured, along with the distributions of vertical and horizontal grain velocities. The velocity distributions showed modest deviations from Maxwell-Boltzmann statistics, except for the vertical velocity distribution near the sample bottom which was highly skewed and non-Gaussian. Data taken for three values of N_ell and two dimensionless accelerations Gamma=15,18 were fit to a hydrodynamic theory, which successfully models the density and temperature profiles including a temperature inversion near the free upper surface.Comment: 14 pages, 15 figure

A sequential quadratic penalty method for nonlinear semidefinite programming

2003-2004 > Academic research: refereed > Publication in refereed journa