Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control. View Full-Tex

Rotating Convection in an Anisotropic System

We study the stability of patterns arising in rotating convection in weakly anisotropic systems using a modified Swift-Hohenberg equation. The anisotropy, either an endogenous characteristic of the system or induced by external forcing, can stabilize periodic rolls in the K\"uppers-Lortz chaotic regime. For the particular case of rotating convection with time-modulated rotation where recently, in experiment, chiral patterns have been observed in otherwise K\"uppers-Lortz-unstable regimes, we show how the underlying base-flow breaks the isotropy, thereby affecting the linear growth-rate of convection rolls in such a way as to stabilize spirals and targets. Throughout we compare analytical results to numerical simulations of the Swift-Hohenberg equation

Vacuum Induced Coherences in Radiatively Coupled Multilevel Systems

We show that radiative coupling between two multilevel atoms having near-degenerate states can produce new interference effects in spontaneous emission. We explicitly demonstrate this possibility by considering two identical V systems each having a pair of transition dipole matrix elements which are orthogonal to each other. We discuss in detail the origin of the new interference terms and their consequences. Such terms lead to the evolution of certain coherences and excitations which would not occur otherwise. The special choice of the orientation of the transition dipole matrix elements enables us to illustrate the significance of vacuum induced coherence in multi-atom multilevel systems. These coherences can be significant in energy transfer studies.Comment: 13 pages including 8 figures in Revtex; submitted to PR

Flat photonic bands in guided modes of textured metallic microcavities

M. G. Salt and William L. Barnes, Physical Review B, Vol. 61, pp. 11125-11135 (2000). "Copyright © 2000 by the American Physical Society."A detailed experimental study of how wavelength-scale periodic texture modifies the dispersion of the guided modes of λ/2 metal-clad microcavities is presented. We first examine the case of a solid-state microcavity textured with a single, periodic corrugation. We explore how the depth of the corrugation and the waveguide thickness affect the width of the band gap produced in the dispersion of the guided modes by Bragg scattering off the periodic structure. We demonstrate that the majority of the corrugation depths studied dramatically modify the dispersion of the lowest-order cavity mode to produce a series of substantially flat bands. From measurements of how the central frequency of the band gap varies with direction of propagation of the guided modes, we determine a suitable two-dimensional texture profile for the production of a complete band gap in all directions of propagation. We then experimentally examine band gaps produced in the guided modes of such a two-dimensionally textured microcavity and demonstrate the existence of a complete band gap for all directions of propagation of the lowest-order TE-polarized mode. We compare our experimental results with those from a theoretical model and find good agreement. Implications of these results for emissive microcavity devices such as light-emitting diodes are discussed

Detection of Epidemic Scarlet Fever Group A Streptococcus in Australia.

Sentinel hospital surveillance was instituted in Australia to detect the presence of pandemic group A Streptococcus strains causing scarlet fever. Genomic and phylogenetic analyses indicated the presence of an Australian GAS emm12 scarlet fever isolate related to United Kingdom outbreak strains. National surveillance to monitor this pandemic is recommended

Organoklorirani pesticidi u slatkovodnim ribama zagrebačkog područja

The aim of this study was to determine the level of organochlorine pesticides in freshwater fish from the Zagreb area, Croatia. The study included 215 freshwater fish samples from three sites: the Sava River, Lake Jarun, and five fishponds from the Zagreb surroundings. Organochlorine pesticides DDT and derivates, HCH, HCB, lindane, aldrin, dieldrin, endrin, heptachlor with epoxide, and methoxychlor were determined using the GC-ECD method. The determined amounts of organochlorine pesticides were within allowed concentration limits in all analysed fish samples. Median values ranged from below the detection limit of 0.01 µg kg-1 for dieldrin and metoxychlor to 2.00 µg kg-1 for DDT in the Cyprinidae fish family from the Sava River, Zagreb sampling site (group 1). This study has confirmed pesticide persistence in the overall ecosystem in our country despite the ban of some thirty years ago, like in many other parts of the world.Cilj istraživanja bio je utvrditi količinu organokloriranih pesticida u slatkovodnim ribama zagrebačkog područja. Obrađeno je ukupno 215 uzoraka slatkovodne ribe sa sljedećih triju lokacija: rijeka Sava, jezero Jarun i pet tzv. ekoloških jezera u okolici Zagreba. Organoklorirani pesticidi DDT i derivati, HCH izomeri (α-HCH, β-HCH and δ-HCH), HCB, lindan (γ-HCH), aldrin, dieldrin, endrin, heptaklor, heptaklorepoksid i metoksiklor) određivali su se metodom plinske kromatografije uz elektronapsorpcijski način detekcije i uz postignutu granicu detekcije od 0,01 µg kg-1. Vrijednosti ispitivanih organokloriranih pesticida u svim su uzorcima riba bile mnogo niže od maksimalno dopuštenih koncentracija. Vrijednosti medijana kretale su se od najnižih 0,01 µg kg-1 za dieldrin i metoksiklor do najviših 2,00 µg kg-1 za DDT u uzorcima riba porodice Cyprinidae s lokacije Sava - Zagreb. Utvrđeni ostaci preostalih ispitivanih pesticida potvrđuju kako njihovu uporabu na našim područjima tako i njihovu postojanost i prisutnost u cjelokupnom ekosustavu unatoč činjenici da je većina zabranjena u Hrvatskoj prije gotovo 30 godina, kao i u mnogim dijelovima svijeta

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies

Molecular fluorescence above metallic gratings

P. Andrew and William L. Barnes, Physical Review B, Vol. 64, article 125405 (2001). "Copyright © 2001 by the American Physical Society."We present measurements of the fluorescence of emitters located in close proximity (d<λ) to metallic grating surfaces. By measuring both the spontaneous emission lifetime and angle-dependent radiation pattern of a monolayer of dye molecules as a function of their separation from planar and periodically corrugated mirrors of increasing modulation depth, we are able to examine the effect of varying the surface profile on the emission process. Both the distance dependence of the lifetime and the spatial distribution of the emitted light are significantly changed upon the introduction of a corrugation, quite apart from the appearance of the familiar Bragg-scattered bound-mode features. It is postulated that these perturbations arise from the interference of the grating scattered dipole fields with the usual upward propagating and reflected fields. In addition, the measurement of nonexponential decay transients for the deepest gratings examined provide evidence for the existence of optically dissimilar dipole positions above the grating surface