bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of double-hybrid energy functionals for π-conjugated systems
Authors: Sancho-García J. C. , Pérez-Jiménez A. J.
Published: August 2009

There have been tremendous efforts in the past decade on the use of computational methods for conjugated systems. Their properties and energetics are often described by density functional theory calculations which, however, are known to face a challenge when dealing with these systems since serious and systematic errors with popular density functionals occur, specially in the case of having stacked or sterically overcrowded aromatic systems, and discourage their use as a black box technique. We overcome here this shortcoming by applying recently developed dispersion-corrected double-hybrid density functionals (B2PLYP) in search of greater yet wide accuracy with little more computational effort. Interestingly, we have derived a related method (B2πPLYP), which has been thoroughly assessed against a set of databases and reactions of the most interest, and works better for this subclass of systems. The deviations with respect to benchmark or experimental values are found to be in the reasonably low range of 1–2 kcal/mol when a correction for the dispersion interactions is added and, most importantly, without suffering the large and systematic errors that are common in former yet conventional methods.
Short wavelength ion temperature gradient mode and coupling with trapped electrons
Authors: Chowdhury J. , Ganesh R. , Vaclavik J. , Brunner S. , Villard L. , Angelino P.
Published: August 2009

The effect of trapped electrons on the ion temperature gradient (ITG) mode in a regime where its wavelength is shorter than the conventional ITG mode (k⊥ρLi≤1) has been studied. Such a mode propagates in the ion diamagnetic direction with a typical scale length k⊥ρLi⪢1 and is termed as the short wavelength ITG (SWITG) mode. The effect of the trapped electrons on this SWITG mode is investigated, for the first time, using a global and local linear gyrokinetic model. The trapped electrons are observed to destabilize the mode strongly. Comparison of the various parameter scans for the SWITG mode with and without the trapped electrons is presented. One important result obtained is that, while in the absence of the trapped electrons the mode was found to subside with increasing value of ϵn=Ln/R exhibiting the character of a slablike mode, the presence of the trapped electrons has been observed to enhance the ϵn=Ln/R window of the existence of the SWITG mode making the mode more toroidal like.
Microassembly based on hands free origami with bidirectional curvature
Authors: Bassik Noy , Stern George M. , Gracias David H.
Published: August 2009

Microassembly based on origami, the Japanese art of paper folding, presents an attractive methodology for constructing complex three-dimensional (3D) devices and advanced materials. A variety of functional structures have been created using patterned metallic, semiconducting, and polymeric thin films, but have been limited to those that curve in a single direction. We report a design framework that can be used to achieve spontaneous bidirectional folds with any desired angle, and we demonstrate theoretical and experimental realizations of complex 3D structures with +90°, −90°, +180°, and −180° folds. The strategy is parallel, versatile, and compatible with conventional microfabrication.
Self-organization of polymer nanoneedles into large-area ordered flowerlike arrays
Authors: Wu Dong , Chen Qi-Dai , Xu Bin-Bin , Jiao Jian , Xu Ying , Xia Hong , Sun Hong-Bo
Published: August 2009

Combination of top-down and bottom-up process is crucial for fabricating ordered complex micronanostructures. Here we report a simple, rapid, and versatile approach to demonstrate this useful concept, which involves the joint use of multibeam interference patterning and capillary force self-organization. Regular hydrophobic arrays of four-peddle nanoflowers consisting of bent needles with 300 nm tip diameters are readily produced. A “domino model” based on the balance of the capillary and support forces were proposed to interpret realization of large-area homogeneity of the array. The technology, promising for preparing more complex and functional structures, may find broad utilization in nano and biological researches.
Particle image velocimetry characterization of turbulent channel flow with rib patterned superhydrophobic walls
Authors: Woolford B. , Prince J. , Maynes D. , Webb B. W.
Published: August 2009

This paper reports particle image velocimetry (PIV) measurements characterizing turbulent flow in a channel with superhydrophobic surfaces, structured and wetting surfaces, and smooth bottom surfaces. The superhydrophobic and structured surfaces are fabricated with alternating ribs and cavities. Both longitudinal and transverse rib/cavity orientations were considered and the surfaces were made superhydrophobic by application of a Teflon coating. The widths of the ribs and cavities were 8 and 32μm, respectively, and the depth of the cavities was 15μm. PIV measurements were acquired for all surfaces considered over the Reynolds numbers range from 4800 to 10 000. Results from the smooth bottom wall measurements were used as a basis for comparison. The hydraulic diameter of the channel was nominally 8.2mm with an aspect ratio of 8.9. The PIV data captured aggregate velocities over multiple rib/cavity modules, such that a spanwise-averaged (over the width of the laser beam) velocity profile was obtained at the channel centerline. The time-averaged velocity profiles reveal no discernible time-mean slip velocity at the superhydrophobic wall. However, the different surfaces are shown to exhibit a systematic influence on the turbulence intensities, total and turbulent shear stress distributions, turbulence production in the channel, and local friction factors. Superhydrophobic surfaces with the ribs and cavities aligned with the flow are shown to yield an 11% decrease in the friction factor while the same surfaces aligned in the transverse direction are shown to cause a modest increase in the friction factor.
Inducing intrinsic localized modes in microelectromechanical cantilever arrays by frequency modulation
Authors: Chen Qingfei , Lai Ying-Cheng , Dietz David
Published: August 2009

We articulate a control method to induce intrinsic localized modes at programable bielement cell in driven microcantilever arrays. The idea is to excite a preassigned cantilever to an oscillating state with significantly higher amplitude than the average by using feedback signal to modulate the frequency that drives the whole array. Our control method is thus global, which is advantageous in microsystems as local pinning actuation may be difficult to implement at small scales.
Exact two-component relativistic theory for nuclear magnetic resonance parameters
Authors: Sun Qiming , Liu Wenjian , Xiao Yunlong , Cheng Lan
Published: August 2009

An exact two-component (X2C) relativistic theory for nuclear magnetic resonance parameters is obtained by first a single block-diagonalization of the matrix representation of the Dirac operator in a magnetic-field-dependent basis and then a magnetic perturbation expansion of the resultant two-component Hamiltonian and transformation matrices. Such a matrix formulation is not only simple but also general in the sense that the various ways of incorporating the field dependence can be treated in a unified manner. The X2C dia- and paramagnetic terms agree individually with the corresponding four-component ones up to machine accuracy for any basis.
Electroluminescence from Ge on Si substrate at room temperature
Authors: Hu Weixuan , Cheng Buwen , Xue Chunlai , Xue Haiyun , Su Shaojian , Bai Anqi , Luo Liping , Yu Yude , Wang Qiming
Published: August 2009

A Ge/Si heterojunction light emitting diode with a p+-Ge/i-Ge/N+–Si structure was fabricated using the ultrahigh vacuum chemical vapor deposition technology on N+–Si substrate. The device had a good I-V rectifying behavior. Under forward bias voltage ranging from 1.1 to 2.5 V, electroluminescence around 1565 nm was observed at room temperature. The mechanism of the light emission is discussed by the radiative lifetime and the scattering rate. The results indicate that germanium is a potential candidate for silicon-based light source material.
Photonic bandgap engineering with inverse opal multistacks of different refractive index contrasts
Authors: Hwang Dae-Kue , Noh Heeso , Cao Hui , Chang Robert P. H.
Published: August 2009

We have self-assembled photonic crystal with a multistack structure using same size of spheres but from materials with different refractive indices. Al2O3, ZnO, and TiO2 are infiltrated into opal templates by atomic layer deposition. Stacking multiple inverse opal structures with different refractive index contrasts broadens the reflection bands dramatically. Numerical simulations with plane wave expansion method show good agreement with experimental results.
Characterization of the quality of ZnO thin films using reflective second harmonic generation
Authors: Huang Yi-Jen , Lo Kuang-Yao , Liu Chung-Wei , Liu Chun-Chu , Chu Sheng-Yuan
Published: August 2009

A polar mirror symmetrical contribution originated from the arrangement of grain boundaries existing in the ZnO film is detected by reflective second harmonic generation pattern. The ordering of ZnO grain boundary is dependent on the kinetic energy of deposited atoms and affects the quality of ZnO films. The net direction of the grain boundary in ZnO film trends toward the [1¯10] direction of Si(111) to reach the minimum grain energy for better quality ZnO film. The polar structure of the mirrorlike boundaries under the optically macroscopic viewpoint presents a correlation with film quality.
Semiconductor quantum dots through conversion of micelle-generated metal clusters
Authors: Wahl D. , Ladenburger A. , Feneberg M. , Schoch W. , Thonke K. , Sauer R.
Published: August 2009

We introduce a method of producing semiconductor quantum dots that is essentially based on the conversion of metal clusters into semiconductor clusters. In the first step, metal dots are generated with the help of self-organizing diblock-copolymers. Then, in the second step, these metal dots are converted into traditional III-V or II-VI semiconductor quantum dots by adding the nonmetallic component. Unlike the commonly used Stranski–Krastanow growth method, our approach completely avoids the formation of an underlying wetting layer. It works basically for any combination of substrate and dot materials being independent of differences in the lattice constants of substrate and dots as are essential for the Stranski–Krastanow growth. Also, the self-ordering of the diblock copolymers is imposed on the metal dots and is retained during their conversion to the semiconductor dots. The dots form an array with average sizes and distances controlled by the partial length of the polymer chains allowing high flexibility for future applications.
Confinement, overflow, and emission of holes on SiGe surface with Ge dots: Heterogeneous hole redistribution and its application to virtual dot manipulation
Authors: Ishii Masashi , Dhesi Sarnjeet S. , Hamilton Bruce
Published: August 2009

The hole confinement in Ge dots fabricated on a wetting layer in Stranski–Krastanov (S-K) growth was directed by an applied bias. At medium bias voltage, the holes overflowed from the small dots, indicating a moderate potential barrier without a notch at the boundary. The electrostatic force of the confined holes attracted excessive holes to the wetting layer. The system was energetically stabilized by the formation of a “virtual dot” in an open space enclosed by dots. At a high bias voltage, the virtual dot disappeared since the holes in the wetting layer were emitted from the surface.
The genus Lithophyllum (Lithophylloideae, Corallinaceae, Rhodophyta) in south-eastern Australia, with the description of L. riosmenae, sp. nov.
Authors: Harvey A. S. , Woelkerling Wm J. , Millar A. J. K.
Published: August 2009

The genus Lithophyllum (Lithophylloideae, Corallinaceae, Rhodophyta) is represented by six species in south-eastern Australia L. chamberlainianum Woelkerling & Campbell, L. corallinae (Crouan & Crouan) Heydrich, L. cuneatum Keats, L. pustulatum (Lamouroux) Foslie, L. riosmenae, sp. nov., and L. stictaeforme (Areschoug in Agardh) Hauck. Four of these taxa are commonly found in Australia, whereas L. cuneatum was previously known only from Fiji and L. riosmenae is newly described. Morphological and anatomical accounts are provided, including keys, information on distribution, nomenclature and habitat in south-eastern Australia. South-eastern Australian species are primarily delimited on characters relating to tetrasporangial conceptacles and the presence/absence of a semi-endophytic habit. Ten species of Lithophyllum are now confirmed to occur in Australia and their diagnostic characters are detailed. Confirmed Australian species of Lithophyllum are primarily delimited on characters relating to tetrasporangial conceptacles, the presence/absence of a semi-endophytic habit and the growth-form. Biogeographic comparisons between south-eastern Australia and other Australian biogeographic regions are also made. Eight species of Lithophyllum are known to occur in southern Australia, three in tropical eastern Australia and three in subtropical western Australia. Southern and south-eastern Australia show major overlap, with five species occurring in both regions. L. pustulatum and L. stictaeformae are widely distributed, having been confirmed to occur in eastern tropical, western subtropical, warm temperate and cold temperate waters within Australia.
Infrageneric phylogeny of Chloantheae (Lamiaceae) based on chloroplast ndhF and nuclear ITS sequence data
Authors: Conn B. J. , Streiber N. , Brown E. A. , Henwood M. J. , Olmstead R. G.
Published: August 2009

The tribe Chloantheae (Prostantheroideae, Lamiaceae) currently consists of over 100 species in nine genera, all of which are endemic to Australia. Generic delimitations were assessed using chloroplast 3′ndhF and nuclear ITS nucleotide sequence data for up to seventy species. Analyses of the two datasets, independently and in combination, used maximum parsimony and Bayesian phylogenetic inference methods. Topologies derived from each marker were broadly congruent, but better resolution and stronger branch support was achieved by combining the datasets. The monophyly of the Chloantheae was confirmed. Brachysola is sister to the rest of the tribe and Chloanthes, Cyanostegia and Dicrastylis (including Mallophora) are monophyletic. Although the species within Dicrastylis were only partially resolved, it appears likely that the current sectional classification of this genus will require revision. A clade containing Newcastelia, Physopsis and Lachnostachys (=Physopsideae) was recovered, but the topology indicates that the current generic circumscriptions need further investigation. A close relationship between Hemiphora elderi, Pityrodia bartlingii and P. uncinata was resolved and reflects their palynological and carpological similarities. The relationship between remaining species of Pityrodia was incompletely resolved.
On the fluctuations that drive small ions toward, and away from, interfaces between polar liquids and their vapors
Authors: Noah-Vanhoucke Joyce , Geissler Phillip L.
Published: September 2009

Contrary to the expectations from classic theories of ion solvation, spectroscopy and computer simulations of the liquid–vapor interface of aqueous electrolyte solutions suggest that ions little larger than a water molecule can prefer to reside near the liquid's surface. Here we advance the view that such affinity originates in a competition between strong opposing forces, primarily due to volume exclusion and dielectric polarization, that are common to all dense polar liquids. We present evidence for this generic mechanism from computer simulations of (
i
) water and (
ii
) a Stockmayer fluid near its triple point. In both cases, we show that strong surface enhancement of small ions, obtained by tuning solutes' size and charge, can be accentuated or suppressed by modest changes in either of those parameters. Statistics of solvent polarization, when the ion is held at and above the Gibbs dividing surface, highlight a basic deficiency in conventional models of dielectric response, namely, the neglect of interfacial flexibility. By distorting the solution's boundary, an ion experiences fluctuations in electrostatic potential and in electric field whose magnitudes attenuate much more gradually (as the ion is removed from the liquid phase) than for a quiescent planar interface. As one consequence, the collective responses that determine free energies of solvation can resolve very differently in nonuniform environments than in bulk. We show that this persistence of electric-field fluctuations additionally shapes the sensitivity of solute distributions to ion polarizability.
Temperature dependence of proton permeation through a voltage-gated proton channel
Authors: Kuno Miyuki , Ando Hiroyuki , Morihata Hirokazu , Sakai Hiromu , Mori Hiroyuki , Sawada Makoto , Oiki Shigetoshi
Published: August 2009

Voltage-gated proton channels are found in many different types of cells, where they facilitate proton movement through the membrane. The mechanism of proton permeation through the channel is an issue of long-term interest, but it remains an open question. To address this issue, we examined the temperature dependence of proton permeation. Under whole cell recordings, rapid temperature changes within a few milliseconds were imposed. This method allowed for the measurement of current amplitudes immediately before and after a temperature jump, from which the ratios of these currents (Iratio) were determined. The use of Iratio for evaluating the temperature dependence minimized the contributions of factors other than permeation. Temperature jumps of various degrees (ΔT, −15 to 15°C) were applied over a wide temperature range (4–49°C), and the Q10s for the proton currents were evaluated from the Iratios. Q10 exhibited a high temperature dependence, varying from 2.2 at 10°C to 1.3 at 40°C. This implies that processes with different temperature dependencies underlie the observed Q10. A novel resistivity pulse method revealed that the access resistance with its low temperature dependence predominated in high temperature ranges. The measured temperature dependence of Q10 was decomposed into Q10 of the channel and of the access resistances. Finally, the Q10 for proton permeation through the voltage-gated proton channel itself was calculated and found to vary from 2.8 at 5°C to 2.2 at 45°C, as expected for an activation enthalpy of 64 kJ/mol. The thermodynamic features for proton permeation through proton-selective channels were discussed for the underlying mechanism.
Proton inhibition of unitary currents of vanilloid receptors
Authors: Liu Beiying , Yao Jing , Wang Yingwei , Li Hui , Qin Feng
Published: August 2009

Protons, which are released during inflammation and injury, regulate many receptors and ion channels involved in pain transduction, including capsaicin channels (transient receptor potential vanilloid receptors 1). Whereas extracellular acidification both sensitizes and directly activates the channel, it also causes concomitant reduction of the unitary current amplitudes. Here, we investigate the mechanisms and molecular basis of this inhibitory effect of protons on channel conductance. Single-channel recordings showed that the unitary current amplitudes decreased with extracellular pH in a dose-dependent manner, consistent with a model in which protons bind to a site within the channel with an apparent pKa of ∼6. The inhibition was voltage dependent, ∼65% at −60 mV and 37% at +60 mV when pH was reduced from 7.4 to 5.5. The unitary current amplitudes reached saturation at [K+] ≥ 1 M, and notably the maximum amplitudes did not converge with different pHs, inconsistent with a blockade model based on surface charge screening or competitive inhibition of permeating ions. Mutagenesis experiments uncovered two acidic residues critical for proton inhibition, one located at the pore entrance and the other on the pore helix. Based on homology to the KcsA structure, the two acidic residues, along with another basic residue also on the pore helix, could form a triad interacting with each other through extensive hydrogen bonds and electrostatic contacts, suggesting that protons may mediate the interactions between the selectivity filter and pore helix, thereby altering the local structure in the filter region and consequently the conductance of the channel.
Fast and slow gating are inherent properties of the pore module of the K+ channel Kcv
Authors: Abenavoli Alessandra , DiFrancesco Mattia Lorenzo , Schroeder Indra , Epimashko Svetlana , Gazzarrini Sabrina , Hansen Ulf Peter , Thiel Gerhard , Moroni Anna
Published: August 2009

Kcv from the chlorella virus PBCV-1 is a viral protein that forms a tetrameric, functional K+ channel in heterologous systems. Kcv can serve as a model system to study and manipulate basic properties of the K+ channel pore because its minimalistic structure (94 amino acids) produces basic features of ion channels, such as selectivity, gating, and sensitivity to blockers. We present a characterization of Kcv properties at the single-channel level. In symmetric 100 mM K+, single-channel conductance is 114 ± 11 pS. Two different voltage-dependent mechanisms are responsible for the gating of Kcv. “Fast” gating, analyzed by β distributions, is responsible for the negative slope conductance in the single-channel current–voltage curve at extreme potentials, like in MaxiK potassium channels, and can be explained by depletion-aggravated instability of the filter region. The presence of a “slow” gating is revealed by the very low (in the order of 1–4%) mean open probability that is voltage dependent and underlies the time-dependent component of the macroscopic current.
Transmission of Bacterial Infections to Healthcare Workers during Intubation and Respiratory Care of Patients with Severe Pneumonia
Authors: Baba Hisashi , Iinuma Yoshitsugu , Imaizumi Kazuyoshi , Hasegawa Yoshinori , Hasegawa Tadao , Ohta Michio , Paterson David L.
Published: August 2009

Exposure of healthcare workers to patients with rapidly fatal infections invariably raises concerns regarding the risk of occupational acquisition. We describe acquisition of Streptococcus pyogenes by 2 nurses from a patient with fatal pneumonia and review previously reported cases of transmission of bacterial pathogens from patients with pneumonia to healthcare workers.
Stress Ulcer Prophylaxis and Ventilation Pneumonia Prevention by Antibacterial Cytoprotective Agents?
Authors: Daschner F. , Kappstein I. , Engels I. , Reuschenbach K. , Pfisterer J. , Krieg N. , Vogel W.
Published: September 2009

The gastric and tracheal flora of 142 consecutive patients receiving stress ulcer prophylaxis were investigated, identifying identical isolates by typing. Furthermore, the growth pattern of normal respiratory bacteria and organisms causing ventilation pneumonia at different pH values and the in vitro effect of sucralfate and bismuth subsalicylate on these bacteria in simulated gastric fluid were studied. The results obtained were as follows: (1) with rising gastric pH bacterial counts in gastric aspirates, especially gram-negatives, increased significantly; (2) in 45 (31.7%) of the patients identical organisms were first isolated in gastric samples and one to two days later in tracheal secretions; (3) ventilation pneumonia was significantly more frequent in patients with high gastric pH; (4) pathogens causing ventilation pneumonia grew well in simulated gastric fluid at higher pH values, unlike normal respiratory organisms; and (5) sucralfate and bismuth subsalicylate showed antibacterial activity against frequent causative organisms of ventilation pneumonia.
Utilization Review and Management: A Brief Analysis of a Growth Industry
Authors: Credè William B. , Hierholzer Walter J.
Published: September 2009

Inpatient hospital care consumes more than 30% of health insurance dollars regardless of the reimbursement mechanism, be it standarti fee-for-service, preferred provider organization (PPO), or health maintenance organization (HMO). It is understandable that reducing these costs has become the highest priority of health care purchasers, and that utilization review and management, the process of evaluating and attempting to reduce the cost of medical practice, has become a major growth industry with providers and purchasers of health care.
Position Paper: The HIV-Infected Healthcare Worker
Authors: Henderson David K. ,   The Association for Practitioners in Infection Control,   The Society of Hospital Epidemiologists of America
Published: September 2009

Consensus statements bearing on issues related to healthcare workers (HCWs) who are, or may be, infected by the human immunodeficiency virus (HIV) have been developed by the Centers for Disease Control (CDC), the American Medical Association (AMA), the American Academy of Pediatrics, the American Hospital Association (AHA), the American Academy of Orthopedic Surgeons, the American College of Obstetricians and Gynecologists8 and the British working groups. In general, these organizations conclude that few, if any, special procedures are required to accommodate an HIV-infected HCW. All except one oppose routine screening of HCWs for HIV infection; all except one oppose broad practice proscriptions for HIV-infected HCWs. Only one of these consensus statements focuses on the HIV-infected HCW. None address important related questions that confront hospitals and other healthcare institutions. These issues are difficult to resolve because: 1) there are insufficient data to establish a scientific basis for their solution; 2) the questions involve medicolegal, ethical or public relations issues that are beyond the usual scope of scientific consensus body recommendations; and/or 3) the situations occur infrequently. Nevertheless, in actual hospital practice, decisions about these questions, at least occasionally, must be made.
Statistical Analysis of Stratified 2X2 Tables
Authors: Davis Charles S.
Published: September 2009

Previous papers in this series have discussed design and analysis issues for epidemiologic data that can be presented in a 2 × 2 table.‘” the primary focus was on methods for determining the extent of association between a dichotomous disease state and a dichotomous risk factor. methods appropriate for cross-sectional, prospective, and retrospective studies using matched or unmatched samples were described.

In order to study the association between disease status and a dichotomous risk factor, it is often necessary to take into account other variables that may influence either the disease status or the risk factor. For example, Hemming, Overall, and Britt studied the association between the occurrence of nosocomial infections (risk factor) and mortality (disease status) in a large cohort of infants in a newborn intensive care unit. these authors analyzed the data using methods for summarizing the results from a single 2 × 2 table. However, because very low birth weight is associated strongly with both the acquisition of nosocomial infection and mortality, it may be more appropriate to control or adjust for the effects of birthweight.
Misleading the masses: detection of mislabelled and substituted frozen fish products in South Africa
Authors: von der Heyden Sophie , Barendse Jaco , Seebregts Anthony J. , Matthee Conrad A.
Published: August 2009

von der Heyden, S., Barendse, J., Seebregts, A. J., and Matthee, C. A. 2010. Misleading the masses: detection of mislabelled and substituted frozen fish products in South Africa. – ICES Journal of Marine Science, 67: 176–185. Mislabelling poses a threat to the sustainability of seafood supply chains and, when frequent, can significantly affect conservation efforts. Here we identify the most popular fish in the South African market through consumer and retailer surveys and data gathered by a sustainable seafood campaign. Of these species, we tested a number of widely available and generally high-market priced fish, utilizing mtDNA 16S rRNA sequencing. Tests of 178 samples revealed that about half of all fillets are mislabelled. Most problematic was kob, Argyrosomus spp., for which some 84% of fillets provided belonged to other species, including mackerel, croaker, and warehou. Phylogenetic analyses provided strong support that the fillets sold as barracuda and wahoo were probably king mackerel and that red snapper fillets included fillets of river snapper, Lutjanus argentimaculatus, which is a species prohibited for sale in South Africa. We also discovered substitution of yellowtail for dorado. From preliminary population genetic comparisons, some 30% of kingklip samples probably had their origin in New Zealand, rather than southern Africa. The research revealed a market conducive to mislabelling through poor consumer and retailer awareness, and highlighted the value of sustainable seafood campaigns to draw attention to this.
Symptomatology of Iris yellow spot virus in Selected Indicator Hosts
Authors: Bag Sudeep , Pappu H. R.
Published: August 2009

Thrips-transmitted Iris yellow spot virus is an economically important pathogen of onion bulb and seed crops. To better understand the biological diversity of IYSV, several plant species were evaluated for their response to mechanical inoculation with IYSV under controlled greenhouse conditions.

Accepted for publication 3 June 2009. Published 24 August 2009.
Evolution of colour vision in mammals
Authors: Jacobs Gerald H.
Published: August 2009

Colour vision allows animals to reliably distinguish differences in the distributions of spectral energies reaching the eye. Although not universal, a capacity for colour vision is sufficiently widespread across the animal kingdom to provideprima facieevidence of its importance as a tool for analysing and interpreting the visual environment. The basic biological mechanisms on which vertebrate colour vision ultimately rests, the cone opsin genes and the photopigments they specify, are highly conserved. Within that constraint, however, the utilization of these basic elements varies in striking ways in that they appear, disappear and emerge in altered form during the course of evolution. These changes, along with other alterations in the visual system, have led to profound variations in the nature and salience of colour vision among the vertebrates. This article concerns the evolution of colour vision among the mammals, viewing that process in the context of relevant biological mechanisms, of variations in mammalian colour vision, and of the utility of colour vision.
Evolution and the origin of the visual retinoid cycle in vertebrates
Authors: Kusakabe Takehiro G. , Takimoto Noriko , Jin Minghao , Tsuda Motoyuki
Published: August 2009

Absorption of a photon by visual pigments induces isomerization of 11-cis-retinaldehyde (RAL) chromophore to all-trans-RAL. Since the opsins lacking 11-cis-RAL lose light sensitivity, sustained vision requires continuous regeneration of 11-cis-RAL via the process called ‘visual cycle’. Protostomes and vertebrates use essentially different machinery of visual pigment regeneration, and the origin and early evolution of the vertebrate visual cycle is an unsolved mystery. Here we compare visual retinoid cycles between different photoreceptors of vertebrates, including rods, cones and non-visual photoreceptors, as well as between vertebrates and invertebrates. The visual cycle systems in ascidians, the closest living relatives of vertebrates, show an intermediate state between vertebrates and non-chordate invertebrates. The ascidian larva may use retinochrome-like opsin as the major isomerase. The entire process of the visual cycle can occur inside the photoreceptor cells with distinct subcellular compartmentalization, although the visual cycle components are also present in surrounding non-photoreceptor cells. The adult ascidian probably uses RPE65 isomerase, andtrans-to-cisisomerization may occur in distinct cellular compartments, which is similar to the vertebrate situation. The complete transition to the sophisticated retinoid cycle of vertebrates may have required acquisition of new genes, such as interphotoreceptor retinoid-binding protein, and functional evolution of the visual cycle genes.
The evolution of irradiance detection: melanopsin and the non-visual opsins
Authors: Peirson Stuart N. , Halford Stephanie , Foster Russell G.
Published: August 2009

Circadian rhythms are endogenous 24 h cycles that persist in the absence of external time cues. These rhythms provide an internal representation of day length and optimize physiology and behaviour to the varying demands of the solar cycle. These clocks require daily adjustment to local time and the primary time cue (zeitgeber) used by most vertebrates is the daily change in the amount of environmental light (irradiance) at dawn and dusk, a process termed photoentrainment. Attempts to understand the photoreceptor mechanisms mediating non-image-forming responses to light, such as photoentrainment, have resulted in the discovery of a remarkable array of different photoreceptors and photopigment families, all of which appear to use a basic opsin/vitamin A-based photopigment biochemistry. In non-mammalian vertebrates, specialized photoreceptors are located within the pineal complex, deep brain and dermal melanophores. There is also strong evidence in fish and amphibians for the direct photic regulation of circadian clocks in multiple tissues. By contrast, mammals possess only ocular photoreceptors. However, in addition to the image-forming rods and cones of the retina, there exists a third photoreceptor system based on a subset of melanopsin-expressing photosensitive retinal ganglion cells (pRGCs). In this review, we discuss the range of vertebrate photoreceptors and their opsin photopigments, describe the melanopsin/pRGC system in some detail and then finally consider the molecular evolution and sensory ecology of these non-image-forming photoreceptor systems.
Evolution of opsins and phototransduction
Authors: Shichida Yoshinori , Matsuyama Take
Published: August 2009

Opsins are the universal photoreceptor molecules of all visual systems in the animal kingdom. They can change their conformation from a resting state to a signalling state upon light absorption, which activates the G protein, thereby resulting in a signalling cascade that produces physiological responses. This process of capturing a photon and transforming it into a physiological response is known as phototransduction. Recent cloning techniques have revealed the rich and diverse nature of these molecules, found in organisms ranging from jellyfish to humans, functioning in visual and non-visual phototransduction systems and photoisomerases. Here we describe the diversity of these proteins and their role in phototransduction. Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules. In particular, we will discuss the evolution of the counterion, the reduction of agonist binding to the receptor, and the molecular properties that characterize rod opsins apart from cone opsins. We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level.
Evolution of phototaxis
Authors: Jékely Gáspár
Published: August 2009

Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present.
Evolution of vertebrate rod and cone phototransduction genes
Authors: Larhammar Dan , Nordström Karin , Larsson Tomas A.
Published: August 2009

Vertebrate cones and rods in several cases use separate but related components for their signal transduction (opsins, G-proteins, ion channels, etc.). Some of these proteins are also used differentially in other cell types in the retina. Because cones, rods and other retinal cell types originated in early vertebrate evolution, it is of interest to see if their specific genes arose in the extensive gene duplications that took place in the ancestor of the jawed vertebrates (gnathostomes) by two tetraploidizations (genome doublings). The ancestor of teleost fishes subsequently underwent a third tetraploidization. Our previously reported analyses showed that several gene families in the vertebrate visual phototransduction cascade received new members in the basal tetraploidizations. We here expand these data with studies of additional gene families and vertebrate species. We conclude that no less than 10 of the 13 studied phototransduction gene families received additional members in the two basal vertebrate tetraploidizations. Also the remaining three families seem to have undergone duplications during the same time period but it is unclear if this happened as a result of the tetraploidizations. The implications of the many early vertebrate gene duplications for functional specialization of specific retinal cell types, particularly cones and rods, are discussed.
Eye evolution: common use and independent recruitment of genetic components
Authors: Vopalensky Pavel , Kozmik Zbynek
Published: August 2009

Animal eyes can vary in complexity ranging from a single photoreceptor cell shaded by a pigment cell to elaborate arrays of these basic units, which allow image formation in compound eyes of insects or camera-type eyes of vertebrates. The evolution of the eye requires involvement of several distinct components—photoreceptors, screening pigment and genes orchestrating their proper temporal and spatial organization. Analysis of particular genetic and biochemical components shows that many evolutionary processes have participated in eye evolution. Multiple examples of co-option of crystallins, Gα protein subunits and screening pigments contrast with the conserved role of opsins and a set of transcription factors governing eye development in distantly related animal phyla. The direct regulation of essential photoreceptor genes by these factors suggests that this regulatory relationship might have been already established in the ancestral photoreceptor cell.
The evolution of eyes and visually guided behaviour
Authors: Nilsson Dan-Eric
Published: August 2009

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes.
Evolution of vertebrate retinal photoreception
Authors: Lamb Trevor D.
Published: August 2009

Recent findings shed light on the steps underlying the evolution of vertebrate photoreceptors and retina. Vertebrate ciliary photoreceptors are not as wholly distinct from invertebrate rhabdomeric photoreceptors as is sometimes thought. Recent information on the phylogenies of ciliary and rhabdomeric opsins has helped in constructing the likely routes followed during evolution. Clues to the factors that led the early vertebrate retina to become invaginated can be obtained by combining recent knowledge about the origin of the pathway for dark re-isomerization of retinoids with knowledge of the inability of ciliary opsins to undergo photoreversal, along with consideration of the constraints imposed under the very low light levels in the deep ocean. Investigation of the origin of cell classes in the vertebrate retina provides support for the notion that cones, rods and bipolar cells all originated from a primordial ciliary photoreceptor, whereas ganglion cells, amacrine cells and horizontal cells all originated from rhabdomeric photoreceptors. Knowledge of the molecular differences between cones and rods, together with knowledge of the scotopic signalling pathway, provides an understanding of the evolution of rods and of the rods' retinal circuitry. Accordingly, it has been possible to propose a plausible scenario for the sequence of evolutionary steps that led to the emergence of vertebrate photoreceptors and retina.
The ‘division of labour’ model of eye evolution
Authors: Arendt Detlev , Hausen Harald , Purschke Günter
Published: August 2009

The ‘division of labour’ model of eye evolution is elaborated here. We propose that the evolution of complex, multicellular animal eyes started from a single, multi-functional cell type that existed in metazoan ancestors. This ancient cell type had at least three functions: light detection via a photoreceptive organelle, light shading by means of pigment granules and steering through locomotor cilia. Located around the circumference of swimming ciliated zooplankton larvae, these ancient cells were able to mediate phototaxis in the absence of a nervous system. This precursor then diversified, by cell-type functional segregation, into sister cell types that specialized in different subfunctions, evolving into separate photoreceptor cells, shading pigment cells (SPCs) or ciliated locomotor cells. Photoreceptor sensory cells and ciliated locomotor cells remained interconnected by newly evolving axons, giving rise to an early axonal circuit. In some evolutionary lines, residual functions prevailed in the specialized cell types that mirror the ancient multi-functionality, for instance, SPCs expressing an opsin as well as possessing rhabdomer-like microvilli, vestigial cilia and an axon. Functional segregation of cell types in eye evolution also explains the emergence of more elaborate photosensory–motor axonal circuits, with interneurons relaying the visual information.
Acid-stress-induced changes in enterohaemorrhagic Escherichia coli O157 : H7 virulence
Authors: House B. , Kus J. V. , Prayitno N. , Mair R. , Que L. , Chingcuanco F. , Gannon V. , Cvitkovitch D. G. , Barnett Foster D.
Published: August 2009

Enterohaemorrhagic Escherichia coli (EHEC) O157 : H7 is naturally exposed to a wide variety of stresses including gastric acid shock, and yet little is known about how this stress influences virulence. This study investigated the impact of acid stress on several critical virulence properties including survival, host adhesion, Shiga toxin production, motility and induction of host-cell apoptosis. Several acid-stress protocols with relevance for gastric passage as well as external environmental exposure were included. Acute acid stress at pH 3 preceded by acid adaptation at pH 5 significantly enhanced the adhesion of surviving organisms to epithelial cells and bacterial induction of host-cell apoptosis. Motility was also significantly increased after acute acid stress. Interestingly, neither secreted nor periplasmic levels of Shiga toxin were affected by acid shock. Pretreatment of bacteria with erythromycin eliminated the acid-induced adhesion enhancement, suggesting that de novo protein synthesis was required for the enhanced adhesion of acid-shocked organisms. DNA microarray was used to analyse the transcriptome of an EHEC O157 : H7 strain exposed to three different acid-stress treatments. Expression profiles of acid-stressed EHEC revealed significant changes in virulence factors associated with adhesion, motility and type III secretion. These results document profound changes in the virulence properties of EHEC O157 : H7 after acid stress, provide a comprehensive genetic analysis to substantiate these changes and suggest strategies that this pathogen may use during gastric passage and colonization in the human gastrointestinal tract.
Subinhibitory concentrations of the cationic antimicrobial peptide colistin induce the pseudomonas quinolone signal in Pseudomonas aeruginosa
Authors: Cummins Joanne , Reen F. Jerry , Baysse Christine , Mooij Marlies J. , O'Gara Fergal
Published: August 2009

Colistin is an important cationic antimicrobial peptide (CAMP) in the fight againstPseudomonas aeruginosainfection in cystic fibrosis (CF) lungs. The effects of subinhibitory concentrations of colistin on gene expression inP. aeruginosawere investigated by transcriptome and functional genomic approaches. Analysis revealed altered expression of 30 genes representing a variety of pathways associated with virulence and bacterial colonization in chronic infection. These included response to osmotic stress, motility, and biofilm formation, as well as genes associated with LPS modification and quorum sensing (QS). Most striking was the upregulation of Pseudomonas quinolone signal (PQS) biosynthesis genes, includingpqsH,pqsBandpqsE, and the phenazine biosynthesis operon. Induction of this central component of the QS network following exposure to subinhibitory concentrations of colistin may represent a switch to a more robust population, with increased fitness in the competitive environment of the CF lung.