Bioinformatics tools in predictive ecology: Applications to fisheries

This article is made available throught the Brunel Open Access Publishing Fund - Copygith @ 2012 Tucker et al.There has been a huge effort in the advancement of analytical techniques for molecular biological data over the past decade. This has led to many novel algorithms that are specialized to deal with data associated with biological phenomena, such as gene expression and protein interactions. In contrast, ecological data analysis has remained focused to some degree on off-the-shelf statistical techniques though this is starting to change with the adoption of state-of-the-art methods, where few assumptions can be made about the data and a more explorative approach is required, for example, through the use of Bayesian networks. In this paper, some novel bioinformatics tools for microarray data are discussed along with their ‘crossover potential’ with an application to fisheries data. In particular, a focus is made on the development of models that identify functionally equivalent species in different fish communities with the aim of predicting functional collapse

Total synthesis and structure-activity-relationship of Alternaric acid delivers an herbicide vector

E.M.I and A.J.B.W. thank Syngenta and EPSRC for an iCASE PhD studentship.Global food security is one of the foremost challenges of our time and requires a multifaceted solution. Crop protection strategies are an essential part of this response; however, there is increasing resistance to known modes of action. Since its discovery in 1949, the natural product alternaric acid has been proposed as a starting point for herbicide development. However, this target is undeveloped due to its poor synthetic accessibility and a lack of knowledge of the associated pharmacology. Here we report the discovery of herbicidal compounds from alternaric acid that operate via a potentially unknown mode of action. Development of a total synthesis enabled structure–activity relationship profiling of compound libraries, which, combined with phenotypic screening and molecular modelling data, identified small-molecule lead compounds with enhanced and broader spectrum herbicidal activity than alternaric acid.PostprintPeer reviewe

Total synthesis of (±)-aspidospermidine, (±)-aspidofractinine, (±)-limaspermidine, and (±)-vincadifformine via a cascade and common intermediate strategy

D.L.C. thanks EPSRC and GSK for a Ph.D. studentship.A concise strategy for the total synthesis of several Aspidosperma alkaloids is reported. A Suzuki–Miyaura cross-coupling provides access to a 2-vinyl indole that undergoes a Diels–Alder cascade reaction with butyn-2-one to deliver a pyrroloindoline intermediate. This undergoes cascade amidation, reduction, skeletal rearrangement, and intramolecular Michael addition to provide a common intermediate containing the full framework of the Aspidosperma alkaloids. The utility of this intermediate is shown in the synthesis of four different natural products.Publisher PDFPeer reviewe

The Amplitude of Non-Equilibrium Quantum Interference in Metallic Mesoscopic Systems

We study the influence of a DC bias voltage V on quantum interference corrections to the measured differential conductance in metallic mesoscopic wires and rings. The amplitude of both universal conductance fluctuations (UCF) and Aharonov-Bohm effect (ABE) is enhanced several times for voltages larger than the Thouless energy. The enhancement persists even in the presence of inelastic electron-electron scattering up to V ~ 1 mV. For larger voltages electron-phonon collisions lead to the amplitude decaying as a power law for the UCF and exponentially for the ABE. We obtain good agreement of the experimental data with a model which takes into account the decrease of the electron phase-coherence length due to electron-electron and electron-phonon scattering.Comment: New title, refined analysis. 7 pages, 3 figures, to be published in Europhysics Letter

A Spatially Resolved `Inside-out' Outburst of IP Pegasi

We present a comprehensive photometric dataset taken over the entire outburst of the eclipsing dwarf nova IP Peg in September/October 1997. Analysis of the lightcurves taken over the long rise to the peak-of-outburst shows conclusively that the outburst started near the centre of the disc and moved outwards. This is the first dataset that spatially resolves such an outburst. The dataset is consistent with the idea that long rise times are indicative of such `inside-out' outbursts. We show how the thickness and the radius of the disc, along with the mass transfer rate change over the whole outburst. In addition, we show evidence of the secondary and the irradiation thereof. We discuss the possibility of spiral shocks in the disc; however we find no conclusive evidence of their existence in this dataset.Comment: 8 pages, 8 figures, to be appear in MNRA

Synthesis of 2-BMIDA indoles via heteroannulation : applications in drug scaffold and natural product synthesis

G.E.B. thanks the EPSRC and GSK for a PhD studentship. J.W.B.F. thanks the Leverhulme Trust for postdoctoral funding (RPG-2018-362).A Pd-catalyzed heteroannulation approach for the synthesis of C2 borylated indoles is reported. The process allows access to highly functionalized 2-borylated indole scaffolds with complete control of regioselectivity. The utility of the process is demonstrated in the synthesis of borylated sulfa drugs and in the concise synthesis of the Aspidosperma alkaloid Goniomitine.Publisher PDFPeer reviewe

Neutron Diffraction Structural Study of Ce₂Fe₁₇₋ₓGaₓ

Six samples of Ce2Fe17-xGax with nominal Ga content x equal to 0, 0.3, 0.5, 0.7, 1.0, 2.0 have been studied by powder neutron diffraction at room temperature. Both crystalline and magnetic refinements have been carried out. All six samples adopt the Th2Zn17-type rhombohedral structure. The only additional phase found is α-iron. Gallium atoms are found to have high affinity for the iron 18h site, and are absent from the 9d and 18f sites. The Ga substitution for Fe leads to an expansion of both the a and c axes. The Curie temperature increases from 238 K for Ce2Fe17 to 406 K for Ce2Fe15Ga2. Magnetic refinements on the samples with x = 0.3, 0.5, 0.7, 1.0, and 2.0 reveal that the magnetic moments of the four Fe sites are in the basal plane and that their values increase with increasing Ga content

Full-wave invisibility of active devices at all frequencies

There has recently been considerable interest in the possibility, both theoretical and practical, of invisibility (or "cloaking") from observation by electromagnetic (EM) waves. Here, we prove invisibility, with respect to solutions of the Helmholtz and Maxwell's equations, for several constructions of cloaking devices. Previous results have either been on the level of ray tracing [Le,PSS] or at zero frequency [GLU2,GLU3], but recent numerical [CPSSP] and experimental [SMJCPSS] work has provided evidence for invisibility at frequency $k\ne 0$. We give two basic constructions for cloaking a region $D$ contained in a domain $\Omega$ from measurements of Cauchy data of waves at \p \Omega; we pay particular attention to cloaking not just a passive object, but an active device within $D$, interpreted as a collection of sources and sinks or an internal current.Comment: Final revision; to appear in Commun. in Math. Physic

Catalytic enantioselective synthesis of heterocyclic vicinal fluoroamines using asymmetric protonation : a method development and mechanistic study

Funding: Leverhulme Trust (Grant Number(s): RPG-2015-308), University of St Andrews, University of Manchester.A catalytic enantioselective synthesis of heterocyclic vicinal fluoroamines is reported. A chiral Brønsted acid promotes aza‐Michael addition to fluoroalkenyl heterocycles to give a prochiral enamine intermediate that undergoes asymmetric protonation upon rearomatization. The reaction accommodates a range of azaheterocycles and nucleophiles, generating the C−F stereocentre in high enantioselectivity, and is also amenable to stereogenic C−CF3 bonds. Extensive DFT calculations provided evidence for stereocontrolled proton transfer from catalyst to substrate as the rate‐determining step, and showed the importance of steric interactions from the catalyst's alkyl groups in enforcing the high enantioselectivity. Crystal structure data show the dominance of noncovalent interactions in the core structure conformation, enabling modulation of the conformational landscape. Ramachandran‐type analysis of conformer distribution and Protein Data Bank mining indicated that benzylic fluorination by this approach has the potential to improve the potency of several marketed drugs.Publisher PDFPeer reviewe