Synthesis of Silver Colloids: Experiment and Computational Model

We summarize our recent results that model the formation of uniform spherical silver colloids prepared by mixing iso-ascorbic acid and silver-amine complex solutions in the absence of dispersants. We found that the experimental results can be modeled effectively by the two-stage formation mechanism used previously to model the preparation of colloidal gold spheres. The equilibrium concentration of silver atoms and the surface tension of silver precursor nanocrystals are both treated as free parameters, and the experimental reaction time scale is fit by a narrow region of this two-parameter space. The kinetic parameter required to match the final particle size is found to be very close to that used previously in modeling the formation of uniform gold particles, suggesting that similar kinetics governs the aggregation process. The model also reproduces semi quantitatively the effects of temperature and solvent viscosity on particle synthesis.Comment: 6 pages, 5 figure

EC-FORC: A New Cyclic Voltammetry Based Method for Examining Phase Transitions and Predicting Equilibrium

We propose a new, cyclic-voltammetry based experimental technique that can not only differentiate between discontinuous and continuous phase transitions in an adsorbate layer, but also quite accurately recover equilibrium behavior from dynamic analysis of systems with a continuous phase transition. The Electrochemical first-order reversal curve (EC-FORC) diagram for a discontinuous phase transition (nucleation and growth), such as occurs in underpotential deposition, is characterized by a negative region, while such a region does not exist for a continuous phase transition, such as occurs in the electrosorption of Br on Ag(100). Moreover, for systems with a continuous phase transition, the minima of the individual EC-FORCs trace the equilibrium curve, even at very high scan rates. Since obtaining experimental data for the EC-FORC method would require only a simple reprogramming of the potentiostat used in conventional cyclic-voltammetry experiments, we believe that this method has significant potential for easy, rapid, in-situ analysis of systems undergoing electrochemical deposition.Comment: 8 pages, 4 figures, 211th ECS Meetin

A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds

Methods that assess patterns of phylogenetic relatedness, as well as character distribution and evolution, allow one to infer the ecological processes involved in community assembly. Assuming niche conservatism, assemblages should shift from phylogenetic clustering to evenness with decreasing geographic scale because the relative importance of mechanisms that shape assemblages is hypothesized to be scale-dependent. Whereas habitat filtering is more likely to act at regional scales because of increased habitat heterogeneity that allows sorting of ecologically similar species in contrasting environments, competition is more likely to act at local scales because low habitat heterogeneity provides few opportunities for niche partitioning. We used species lists to assess assemblage composition, data on ecologically-relevant traits, and a molecular phylogeny, to examine the phylogenetic structure of antbird (Thamnophilidae) assemblages at three different geographical scales: regional (ecoregions), intermediate (100-ha plots) and local (mixed-flocks). In addition, we used patterns of phylogenetic beta diversity and beta diversity to separate the factors that structure antbird assemblages at regional scales. Contrary to previous findings, we found a shift from phylogenetic evenness to clustering with decreasing geographical scale. We argue that this does not reject the hypothesis that habitat filtering is the predominant force in regional community assembly, because analyses of trait evolution and structure indicated a lack of niche conservatism in antbirds. In some cases, phylogenetic evenness at regional scales can be an effect of historical biogeographic processes instead of niche-based processes. However, regional patterns of beta diversity and phylogenetic beta diversity suggested that phylogenetic structure in our study cannot be explained by the history of speciation and dispersal of antbirds, further supporting the habitat-filtering hypothesis. Our analyses suggested that competitive interactions might not play an important role locally, which would provide a plausible explanation for the high alpha diversity of antbirds in Amazonia. Finally, we emphasize the importance of including trait information in studies of phylogenetic community structure to adequately assess the mechanisms that determine species co-existence. © 2010 The Authors. Journal compilation © 2010 British Ecological Society

The influence of the complex topography and dynamic history of the montane Neotropics on the evolutionary differentiation of a cloud forest bird (Premnoplex brunnescens, Furnariidae)

Aim: To examine the effect of geographical barriers and habitat dynamics related to climatic oscillations on the phylogeography of a widespread passerine of Neotropical cloud forests, the spotted barbtail (Premnoplex brunnescens). Location: Neotropical humid forests of montane areas in lower Central America and South America. Methods: We sequenced two mitochondrial genes and one nuclear intron from specimens collected across the distribution of P. brunnescens. Phylogenetic relationships were inferred using Bayesian and maximum-likelihood methods. Groups with maximum differentiation were estimated with spatial analysis of molecular variance (SAMOVA). We estimated timing of differentiation and relationships among groups with a species-tree approach and historical demography with extended Bayesian skyline plots. Results: Six highly differentiated clades of P. brunnescens are distributed in lower Central America, Sierra Nevada de Santa Marta, northern Venezuelan mountains, the Northern Andes, central Peru, and southern Peru and Bolivia. Within the Northern Andes clade, six phylogroups were identified associated with different slopes and isolated cordilleras. Most clades occupy opposite sides of low-lying valleys and ridgelines, but little differentiation was observed across several putative barriers. Population divergence occurred in the late Miocene and Pliocene, perhaps in association with Andean uplift. Historical fluctuations in population sizes suggest that populations tracked the spatial dynamics of montane forests associated with glacial cycles. Main conclusions: Extensive genetic differentiation in mitochondrial and nuclear DNA exists among populations of P. brunnescens. Such marked divergence was probably promoted by the rugged topography and dynamic ecological history of the Neotropical mountains. Our study sheds light on mechanisms promoting population differentiation in the montane Neotropics. © 2014 John Wiley & Sons Ltd

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. © 2009 The Willi Hennig Society

Positive association between population genetic differentiation and speciation rates in New World birds

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from173 NewWorld bird species (\u3e17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity

Neural circuitry engaged during unsuccessful motor inhibition in pediatric bipolar disorder

Objective: Deficits in motor inhibition may contribute to impulsivity and irritability in children with bipolar disorder (BPD). Therefore, studies of the neural circuitry engaged during failed motor inhibition in pediatric BPD may contribute to our understanding of the pathophysiology of the illness. We tested the hypothesis that children with BPD and controls would differ in ventral prefrontal cortex (vPFC), striatal, and anterior cingulate activation during unsuccessful motor inhibition. We also compared activation in medicated vs. unmedicated children with BPD, and in children with BPD and ADHD (BPD+ADHD) vs. those with BPD but without ADHD (BPD-ADHD). Method: Event-related fMRI study comparing neural activation in children with BPD and controls while they performed a motor inhibition task. The sample included 26 children with BPD (13 unmedicated, 15 with ADHD) and 17 age, gender, and IQ matched controls. Results: On failed inhibitory trials, controls showed greater bilateral striatal and right vPFC activation than did patients. While our findings were somewhat more prominent in unmedicated than medicated, patients, and in BPD+ADHD than BPD-ADHD, the findings did not differ significantly (?) among these subgroups of children with BPD. Conclusions: Compared to controls, children with BPD may have deficits in their ability to engage striatal structures and right vPFC during unsuccessful inhibition. (this reads confusingly to me—they’re deficient in their capacity to engage structures when they’re behaviorally unsuccessful? Perhaps reword?) Further research is needed to determine whether these deficits play a role in the emotional and behavioral dysregulation characteristic of BPD

Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously