Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed “WoodKing” (woodpeckers/rollers/kingfishers), “SCA” (owls/potoos/owlet-nightjars/hummingbirds/swifts), and “Conglomerati.” In general, the support is highly significant with just two exceptions, the owls move from the “SCA” group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the “Conglomerati”. Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the β-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.

Generation of active surface states of gold and the role of such states in electrocatalysis

The cyclic voltammetry behaviour of gold in aqueous media is often regarded in very simple terms as a combination of two distinct processes, double layer charging/discharging and monolayer oxide formation/removal. This view is questioned here on the basis of both the present results and earlier independent data by other authors. It was demonstrated in the present case that both severe cathodization or thermal pretreatment of polycrystalline gold in acid solution resulted in the appearance of substantial Faradaic responses in the double layer region. Such anamolous behaviour, as outlined recently also for other metals, is rationalized in terms of the presence of active metal atoms (which undergo premonolayer oxidation) at the electrode surface. Such behaviour, which is also assumed to correspond to that of active sites on conventional gold surfaces, is assumed to be of vital importance in electrocatalysis; in many instances the latter process is also quite marked in the double layer region.

Shape dependent electrocatalytic behaviour of silver nanoparticles

The electrochemical and electrocatalytic behaviour of silver nanoprisms, nanospheres and nanocubes of comparable size in an alkaline medium have been investigated to ascertain the shape dependent behaviour of silver nanoparticles, which are an extensively studied nanomaterial. The nanomaterials were synthesised using chemical methods and characterised with UV-visible spectroscopy, transmission electron microscopy and X-ray diffraction. The nanomaterials were immobilised on a substrate glassy carbon electrode and characterised by cyclic voltammetry for their surface oxide electrochemistry. The electrocatalytic oxidation of hydrazine and formaldehyde and the reduction of hydrogen peroxide were studied by performing cyclic voltammetric and chronoamperometric experiments for both the nanomaterials and a smooth polycrystalline macrosized silver electrode. In all cases the nanomaterials showed enhanced electrocatalytic activity over the macro-silver electrode. Significantly, the silver nanoprisms that are rich in hcp lamellar defects showed greater activity than nanospheres and nanocubes for all reactions studied.

The role of defects, or active states, in surface electrochemistry with particular reference to gold in neutral solution

Metastable, active, or nonequilibrium states due to the presence of abnormal structures and various types of defects are well known in metallurgy. The role of such states at gold surfaces in neutral aqueous media (an important electrode system in the microsensor area) was explored using cyclic voltammetry. It was demonstrated that, as postulated in earlier work from this laboratory, there is a close relationship between premonolayer oxidation, multilayer hydrous oxide reduction and electrocatalytic behaviour in the case of this and other metal electrode systems. Some of the most active, and therefore most important, entities at surfaces (e.g., metal adatoms) are not readily imageable or detectable by high resolution surface microscopy techniques. Cyclic voltammetry, however, provides significant, though not highly specific, information about such species. The main conclusion is that further practical and theoretical work on active states of metal surfaces is highly desirable as their behaviour is not simple and is of major importance in many electrocatalytic processes.

AFM study of morphological changes associated with electrochemical solid--solid transformation of three-dimensional crystals of TCNQ to metal derivatives (metal= Cu, Co, Ni; TCNQ= tetracyanoquinodimethane)

In situ atomic force microscopy (AFM) allows images from the upper face and sides of TCNQ crystals to be monitored during the course of the electrochemical solid–solid state conversion of 50 × 50 μm2 three-dimensional drop cast crystals of TCNQ to CuTCNQ or M[TCNQ]2(H2O)2 (M = Co, Ni). Ex situ images obtained by scanning electron microscopy (SEM) also allow the bottom face of the TCNQ crystals, in contact with the indium tin oxide or gold electrode surface and aqueous metal electrolyte solution, to be examined. Results show that by carefully controlling the reaction conditions, nearly mono-dispersed, rod-like phase I CuTCNQ or M[TCNQ]2(H2O)2 can be achieved on all faces. However, CuTCNQ has two different phases, and the transformation of rod-like phase 1 to rhombic-like phase 2 achieved under conditions of cyclic voltammetry was monitored in situ by AFM. The similarity of in situ AFM results with ex situ SEM studies accomplished previously implies that the morphology of the samples remains unchanged when the solvent environment is removed. In the process of crystal transformation, the triple phase solid∣electrode∣electrolyte junction is confirmed to be the initial nucleation site. Raman spectra and AFM images suggest that 100% interconversion is not always achieved, even after extended electrolysis of large 50 × 50 μm2 TCNQ crystals.

Electrochemical detection of dopamine and cytochrome c at a nanostructured gold electrode

A nanostructured gold surface consisting of closely packed outwardly growing spikes is investigated for the electrochemical detection of dopamine and cytochrome c. A significant electrocatalytic effect for the electrooxidation of both dopamine and ascorbic acid at the nanostructured electrode was found due to the presence of surface active sites which allowed the detection of dopamine in the presence of excess ascorbic acid to be achieved by differential pulse voltammetry. By simple modification with a layer of Nafion, the enhanced electrocatalytic properties of the nanostructured surface was maintained while increasing the selectivity of dopamine detection in the presence of interfering species such as excess ascorbic and uric acids. Also, upon modification of the nanostructured surface with a monolayer of cysteine, the electrochemical response of immobilised cytochrome c in two distinct conformations was observed. This opens up the possibility of using such a nanostructured surface for the characterisation of other biomolecules and in bio-electroanalytical applications.

An investigation of silver electrodeposition from ionic liquids : influence of atmospheric water uptake on the silver electrodeposition mechanism and film morphology

The electrodeposition of silver from two ionic liquids, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]) and N-butyl-N-methyl-pyrrolidinium bis(trifluoromethanesulfonyl)imide ([C4mPyr][TFSI]), and an aqueous KNO3 solution on a glassy carbon electrode was undertaken. It was found by cyclic voltammetry that the electrodeposition of silver proceeds through nucleation–growth kinetics. Analysis of chronoamperometric data indicated that the nucleation–growth mechanism is instantaneous at all potentials in the case of [BMIm][BF4] and [C4mPyr][TFSI], and instantaneous at low overpotentials tending to progressive at high overpotentials for KNO3. Significantly, under ambient conditions, the silver electrodeposition mechanism changes to progressive nucleation and growth in [C4mPyr][TFSI], which is attributed to the uptake of atmospheric water in the IL. It was found that these differences in the growth mechanism impact significantly on the morphology of the resultant electrodeposit which is characterised ex situ by scanning electron microscopy and X-ray diffraction.

The active site behaviour of electrochemically synthesised gold nanomaterials

Even though gold is the noblest of metals, a weak chemisorber and is regarded as being quite inert, it demonstrates significant electrocatalytic activity in its nanostructured form. It is demonstrated here that nanostructured and even evaporated thin films of gold are covered with active sites which are responsible for such activity. The identification of these sites is demonstrated with conventional electrochemical techniques such as cyclic voltammetry as well as a large amplitude Fourier transformed alternating current (FT-ac) method under acidic and alkaline conditions. The latter technique is beneficial in determining if an electrode process is either Faradaic or capacitive in nature. The observed behaviour is analogous to that observed for activated gold electrodes whose surfaces have been severely disrupted by cathodic polarisation in the hydrogen evolution region. It is shown that significant electrochemical oxidation responses occur at discrete potential values well below that for the formation of the compact monolayer oxide of bulk gold and are attributed to the facile oxidation of surface active sites. Several electrocatalytic reactions are explored in which the onset potential is determined by the presence of such sites on the surface. Significantly, the facile oxidation of active sites is used to drive the electroless deposition of metals such as platinum, palladium and silver from their aqueous salts on the surface of gold nanostructures. The resultant surface decoration of gold with secondary metal nanoparticles not only indicates regions on the surface which are rich in active sites but also provides a method to form interesting bimetallic surfaces.

Large amplitude Fourier transformed AC voltammetric investigation of the active state electrochemistry of a copper/aqueous base interface and implications for electrocatalysis

The higher harmonic components available from large-amplitude Fourier-transformed alternating current (FT-ac) voltammetry enable the surface active state of a copper electrode in basic media to be probed in much more detail than possible with previously used dc methods. In particular, the absence of capacitance background current allows low-level Faradaic current contributions of fast electron-transfer processes to be detected; these are usually completely undetectable under conditions of dc cyclic voltammetry. Under high harmonic FT-ac voltammetric conditions, copper electrodes exhibit well-defined and reversible premonolayer oxidation responses at potentials within the double layer region in basic 1.0 M NaOH media. This process is attributed to oxidation of copper adatoms (Cu*) of low bulk metal lattice coordination numbers to surface-bonded, reactive hydrated oxide species. Of further interest is the observation that cathodic polarization in 1.0 M NaOH significantly enhances the current detected in each of the fundamental to sixth FT-ac harmonic components in the Cu*/Cu hydrous oxide electron-transfer process which enables the underlying electron transfer processes in the higher harmonics to be studied under conditions where the dc capacitance response is suppressed; the results support the incipient hydrous oxide adatom mediator (IHOAM) model of electrocatalysis. The underlying quasi-reversible interfacial Cu*/Cu hydrous oxide process present under these conditions is shown to mediate the reduction of nitrate at a copper electrode, while the mediator for the hydrazine oxidation reaction appears to involve a different mediator or active state redox couple. Use of FT-ac voltammetry offers prospects for new insights into the nature of active sites and electrocatalysis at the electrode/solution interface of Group 11 metals in aqueous media.

Reduction of Au3+ ions by activated surface atoms of platinum

In this work it is demonstrated that Pt electrodes can be activated by cathodic polarisation in the hydrogen evolution region which makes it prone to oxidation at potentials below that of bulk oxide formation. When an activated Pt electrode is placed in an aqueous HAuCl4 solution the electroless deposition of Au onto the surface of the electrode is observed and confirmed by cyclic voltammetry and XPS measurements. It is demonstrated that the oxidation of active Pt surface atoms provides the driving force for the spontaneous reduction of Au3+ ions into metallic Au to generate a Pt/Au surface which is highly active for the electro-oxidation of ethanol.