Characterization of CO Adsorbed to Clean and Partially Oxidized Cu(211) and Cu(111).

Copper-based catalysts gain activity through the presence of poorly coordinated Cu atoms and incomplete oxidation at the surface. The catalytic mechanisms can in principle be observed by controlled dosing of reactants to single-crystal substrates. However, the interconnected influences of surface defects, partial oxidation, and adsorbate coverage present a large matrix of conditions that have not been fully explored in the literature. We recently characterized oxygen and carbon monoxide coadsorption on Cu(111), a nominally defect-free surface, and now extend our study to the stepped surface Cu(211). Temperature-programmed desorption of CO adsorbed to bare metal surfaces confirms that two sites dominate desorption from a saturated layer: atop terrace atoms of local (111) character and atop step edge atoms with CO bound more strongly to the latter. At low coverage, discrete CO resonances in reflection adsorption infrared spectra can be assigned to these sites: 2077 cm-1 for extended (111) terraces, 2093 cm-1 for step sites, and additional kink-adsorbed molecules at 2110 cm-1. With increasing coverage, in contrast to Cu(111), the infrared spectral features on Cu(211) evolve and shift as a consequence of dipole-dipole coupling between differentially occupied types of sites. Auger electron spectroscopy shows that exposure to background O2 oxidizes the (211) surface at a rate nearly 1 order of magnitude greater than (111); we argue that the resulting surface is stoichiometric Cu2O, as previously found for Cu(111). This oxide binds CO less strongly than the bare metal and the underlying crystal cut continues to influence the adsorption sites available to CO. On oxidized (111) terraces, broad absorption peaks at 2115-2120 cm-1; on oxidized Cu(211), CO adsorbed to step sites appears as a resolved secondary peak at 2144 cm-1. This suite of spectroscopic signatures, obtained under carefully controlled conditions, will help to determine the origin and fate of adsorbed species in future studies of reaction mechanisms on copper.

RAIRS Characterization of CO and O Coadsorption on Cu(111).

In a study preliminary to investigating CO2 dissociation, we report our results on oxygen and carbon monoxide coadsorption on Cu(111). We use reflection adsorption infrared spectroscopy and Auger electron spectroscopy to characterize and quantify adsorbed species. On clean Cu(111), the CO internal stretch mode appears initially at 2077 cm-1 for a surface temperature of ∼80 K. We accurately reproduce the previously determined redshift of the absorption band with increasing CO coverage. We subsequently oxidize the surface by exposure to O2 at 300 K to ensure O2 dissociation. The band's frequency and line shape of subsequently adsorbed CO at ∼80 K are not affected. However, the maximum absorbance and integrated peak intensities drop with increasing O coverage. The data suggest that CO is not adsorbed near O, likely as a consequence of the mechanism of Cu(111) surface oxidation by O2 at 300 K. We discuss whether our RAIRS results may be used to quantify CO2 dissociation in the zero-coverage limit.

Bladderworts, the smallest known suction feeders, generate inertia-dominated flows to capture prey.

Aquatic bladderworts (Utricularia gibba and U. australis) capture zooplankton in mechanically triggered underwater traps. With characteristic dimensions less than 1 mm, the trapping structures are among the smallest known to capture prey by suction, a mechanism that is not effective in the creeping-flow regime where viscous forces prevent the generation of fast and energy-efficient suction flows. To understand what makes suction feeding possible on the small scale of bladderwort traps, we characterised their suction flows experimentally (using particle image velocimetry) and mathematically (using computational fluid dynamics and analytical mathematical models). We show that bladderwort traps avoid the adverse effects of creeping flow by generating strong, fast-onset suction pressures. Our findings suggest that traps use three morphological adaptations: the trap walls' fast release of elastic energy ensures strong and constant suction pressure; the trap door's fast opening ensures effectively instantaneous onset of suction; the short channel leading into the trap ensures undeveloped flow, which maintains a wide effective channel diameter. Bladderwort traps generate much stronger suction flows than larval fish with similar gape sizes because of the traps' considerably stronger suction pressures. However, bladderworts' ability to generate strong suction flows comes at considerable energetic expense.

DNA surface exploration and operator bypassing during target search.

Many proteins that bind specific DNA sequences search the genome by combining three-dimensional diffusion with one-dimensional sliding on nonspecific DNA1-5. Here we combine resonance energy transfer and fluorescence correlation measurements to characterize how individual lac repressor (LacI) molecules explore the DNA surface during the one-dimensional phase of target search. To track the rotation of sliding LacI molecules on the microsecond timescale, we use real-time single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy (SMCT-FCS). The fluctuations in fluorescence signal are accurately described by rotation-coupled sliding, in which LacI traverses about 40 base pairs (bp) per revolution. This distance substantially exceeds the 10.5-bp helical pitch of DNA; this suggests that the sliding protein frequently hops out of the DNA groove, which would result in the frequent bypassing of target sequences. We directly observe such bypassing using single-molecule fluorescence resonance energy transfer (smFRET). A combined analysis of the smFRET and SMCT-FCS data shows that LacI hops one or two grooves (10-20 bp) every 200-700 µs. Our data suggest a trade-off between speed and accuracy during sliding: the weak nature of nonspecific protein-DNA interactions underlies operator bypassing, but also speeds up sliding. We anticipate that SMCT-FCS, which monitors rotational diffusion on the microsecond timescale while tracking individual molecules with millisecond resolution, will be applicable to the real-time investigation of many other biological interactions and will effectively extend the accessible time regime for observing these interactions by two orders of magnitude.

Hydrodynamics of the bladderwort feeding strike.

The aquatic bladderwort Utricularia gibba captures zooplankton in mechanically triggered underwater traps. With characteristic dimensions <1 mm, the trapping structures are among the smallest known that work by suction-a mechanism that would not be effective in the creeping-flow regime. To understand the adaptations that make suction feeding possible on this small scale, we have measured internal flow speeds during artificially triggered feeding strikes in the absence of prey. These data are compared with complementary analytical models of the suction event: an inviscid model of the jet development in time and a steady-state model incorporating friction. The initial dynamics are well described by a time-dependent Bernoulli equation in which the action of the trap door is represented by a step increase in driving pressure. According to this model, the observed maximum flow speed (5.2 m/s) depends only on the pressure difference, whereas the initial acceleration (3 × 104 m/s2 ) is determined by pressure difference and channel length. Because the terminal speed is achieved quickly (~0.2 ms) and the channel is short, the remainder of the suction event (~2.0 ms) is effectively an undeveloped viscous steady state. The steady-state model predicts that only 17% of power is lost to friction. The energy efficiency and steady-state fluid speed decrease rapidly with decreasing channel diameter, setting a lower limit on practical bladderwort size.

Thermodynamics of the Bladderwort Feeding Strike-Suction Power from Elastic Energy Storage.

The carnivorous plant bladderwort exemplifies the use of accumulated elastic energy to power motion: respiration-driven pumps slowly load the walls of its suction traps with elastic energy (∼1 h). During a feeding strike, this energy is released suddenly to accelerate water (∼1 ms). However, due to the traps' small size and concomitant low Reynolds number, a significant fraction of the stored energy may be dissipated as viscous friction. Such losses and the mechanical reversibility of Stokes flow are thought to degrade the feeding success of other suction feeders in this size range, such as larval fish. In contrast, triggered bladderwort traps are generally successful. By mapping the energy budget of a bladderwort feeding strike, we illustrate how this smallest of suction feeders can perform like an adult fish.

Evolution of high-level resistance during low-level antibiotic exposure.

It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.

Variation in Mutational Robustness between Different Proteins and the Predictability of Fitness Effects.

Random mutations in genes from disparate protein classes may have different distributions of fitness effects (DFEs) depending on different structural, functional, and evolutionary constraints. We measured the fitness effects of 156 single mutations in the genes encoding AraC (transcription factor), AraD (enzyme), and AraE (transporter) used for bacterial growth on l-arabinose. Despite their different molecular functions these genes all had bimodal DFEs with most mutations either being neutral or strongly deleterious, providing a general expectation for the DFE. This contrasts with the unimodal DFEs previously obtained for ribosomal protein genes where most mutations were slightly deleterious. Based on theoretical considerations, we suggest that the 33-fold higher average mutational robustness of ribosomal proteins is due to stronger selection for reduced costs of translational and transcriptional errors. Whereas the large majority of synonymous mutations were deleterious for ribosomal proteins genes, no fitness effects could be detected for the AraCDE genes. Four mutations in AraC and AraE increased fitness, suggesting that slightly advantageous mutations make up a significant fraction of the DFE, but that they often escape detection due to the limited sensitivity of commonly used fitness assays. We show that the fitness effects of amino acid substitutions can be predicted based on evolutionary conservation, but those weakly deleterious mutations are less reliably detected. This suggests that large-effect mutations and the fraction of highly deleterious mutations can be computationally predicted, but that experiments are required to characterize the DFE close to neutrality, where many mutations ultimately fixed in a population will occur.

Coverage-dependent adsorption and desorption of oxygen on Pd(100).

We have studied the adsorption and desorption of O2 on Pd(100) by supersonic molecular beam techniques and thermal desorption spectroscopy. Adsorption measurements on the bare surface confirm that O2 initially dissociates for all kinetic energies between 56 and 380 meV and surface temperatures between 100 and 600 K via a direct mechanism. At and below 150 K, continued adsorption leads to a combined O/O2 overlayer. Dissociation of molecularly bound O2 during a subsequent temperature ramp leads to unexpected high atomic oxygen coverages, which are also obtained at high incident energy and high surface temperature. At intermediate temperatures and energies, these high final coverages are not obtained. Our results show that kinetic energy of the gas phase reactant and reaction energy dissipated during O2 dissociation on the cold surface both enable activated nucleation of high-coverage surface structures. We suggest that excitation of local substrate phonons may play a crucial role in oxygen dissociation at any coverage.

Quantification of transcription factor-DNA binding affinity in a living cell.

The apparent dissociation constant (Kd) for specific binding of glucocorticoid receptor (GR) and androgen receptor (AR) to DNA was determined in vivo in Xenopus oocytes. The total nuclear receptor concentration was quantified as specifically retained [(3)H]-hormone in manually isolated oocyte nuclei. DNA was introduced by nuclear microinjection of single stranded phagemid DNA, chromatin is then formed during second strand synthesis. The fraction of DNA sites occupied by the expressed receptor was determined by dimethylsulphate in vivo footprinting and used for calculation of the receptor-DNA binding affinity. The forkhead transcription factor FoxA1 enhanced the DNA binding by GR with an apparent Kd of ∼1 µM and dramatically stimulated DNA binding by AR with an apparent Kd of ∼0.13 µM at a composite androgen responsive DNA element containing one FoxA1 binding site and one palindromic hormone receptor binding site known to bind one receptor homodimer. FoxA1 exerted a weak constitutive- and strongly cooperative DNA binding together with AR but had a less prominent effect with GR, the difference reflecting the licensing function of FoxA1 at this androgen responsive DNA element.

What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

We have investigated which aspects of transcription factor DNA interactions are most important to account for the recent in vivo search time measurements for the dimeric lac repressor. We find the best agreement for a sliding model where non-specific binding to DNA is improbable at first contact and the sliding LacI protein binds at high probability when reaching the specific Osym operator. We also find that the contribution of hopping to the overall search speed is negligible although physically unavoidable. The parameters that give the best fit reveal sliding distances, including hopping, close to what has been proposed in the past, i.e. ∼40 bp, but with an unexpectedly high 1D diffusion constant on non-specific DNA sequences. Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value. This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed. For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.

A shape-recovery polymer coating for the corrosion protection of metallic surfaces.

Self-healing polymer coatings are a type of smart material aimed for advanced corrosion protection of metals. This paper presents the synthesis and characterization of two new UV-cure self-healing coatings based on acrylated polycaprolactone polyurethanes. On a macroscopic scale, the cured films all show outstanding mechanical properties, combining relatively high Young's modulus of up to 270 MPa with a strain at break above 350%. After thermal activation the strained films recover up to 97% of their original length. Optical and electron microscopy reveals the self-healing properties of these coatings on hot dip galvanized steel with scratches and microindentations. The temperature-induced closing of such defects restores the corrosion protection and barrier properties of the coating as shown by electrochemical impedance spectroscopy and scanning vibrating electrode technique. Therefore, such coatings are a complementary option for encapsulation-based autonomous corrosion protection systems.

Desorption of water from distinct step types on a curved silver crystal.

We have investigated the adsorption of H2O onto the A and B type steps on an Ag single crystal by temperature programmed desorption. For this study, we have used a curved crystal exposing a continuous range of surface structures ranging from [5(111) × (100)] via (111) to [5(111) × (110)]. LEED and STM studies verify that the curvature of our sample results predominantly from monoatomic steps. The sample thus provides a continuous array of step densities for both step types. Desorption probed by spatially-resolved TPD of multilayers of H2O shows no dependence on the exact substrate structure and thus confirms the absence of thermal gradients during temperature ramps. In the submonolayer regime, we observe a small and linear dependence of the desorption temperature on the A and B step density. We argue that such small differences are only observable by means of a single curved crystal, which thus establishes new experimental benchmarks for theoretical calculation of chemically accurate binding energies. We propose an origin of the observed behavior based on a "two state" desorption model.

High fitness costs and instability of gene duplications reduce rates of evolution of new genes by duplication-divergence mechanisms.

An important mechanism for generation of new genes is by duplication-divergence of existing genes. Duplication-divergence includes several different submodels, such as subfunctionalization where after accumulation of neutral mutations the original function is distributed between two partially functional and complementary genes, and neofunctionalization where a new function evolves in one of the duplicated copies while the old function is maintained in another copy. The likelihood of these mechanisms depends on the longevity of the duplicated state, which in turn depends on the fitness cost and genetic stability of the duplications. Here, we determined the fitness cost and stability of defined gene duplications/amplifications on a low copy number plasmid. Our experimental results show that the costs of carrying extra gene copies are substantial and that each additional kilo base pairs of DNA reduces fitness by approximately 0.15%. Furthermore, gene amplifications are highly unstable and rapidly segregate to lower copy numbers in absence of selection. Mathematical modeling shows that the fitness costs and instability strongly reduces the likelihood of both sub- and neofunctionalization, but that these effects can be offset by positive selection for novel beneficial functions.

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models.

Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The details of such sliding have largely been beyond direct experimental observation. For this purpose we devised an analytical formulation of umbrella sampling along a helical coordinate, and from extensive and fully atomistic simulations we quantified the free-energy landscapes that underlie the sliding dynamics and dissociation kinetics for the LacI dimer. The resulting potential of mean force distributions show a fine structure with an amplitude of 1 k(B)T for sliding and 12 k(B)T for dissociation. Based on the free-energy calculations the repressor slides in close contact with DNA for 8 bp on average before making a microscopic dissociation. By combining the microscopic molecular-dynamics calculations with Brownian simulation including rotational diffusion from the microscopically dissociated state we estimate a macroscopic residence time of 48 ms at the same DNA segment and an in vitro sliding distance of 240 bp. The sliding distance is in agreement with previous in vitro sliding-length estimates. The in vitro prediction for the macroscopic residence time also compares favorably to what we measure by single-molecule imaging of nonspecifically bound fluorescently labeled LacI in living cells. The investigation adds to our understanding of transcription-factor search kinetics and connects the macro-/mesoscopic rate constants to the microscopic dynamics.

100% thiol-functionalized ethylene PMOs prepared by "thiol acid-ene" chemistry.

A novel thiol functionalized bis-silane PMO precursor was synthesized by highly efficient thiol acid-ene chemistry between the double bonds of 1,2-(E)-bis(triethoxysilyl)ethene and thioacetic acid. After aminolysis the self-assembly process of the formed SH-precursor with Pluronic P123 under acidic conditions yields the first 100% thiol-PMO material with good structural ordering.

Lost in presumption: stochastic reactions in spatial models.

Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems.

Selection-driven gene loss in bacteria.

Gene loss by deletion is a common evolutionary process in bacteria, as exemplified by bacteria with small genomes that have evolved from bacteria with larger genomes by reductive processes. The driving force(s) for genome reduction remains unclear, and here we examined the hypothesis that gene loss is selected because carriage of superfluous genes confers a fitness cost to the bacterium. In the bacterium Salmonella enterica, we measured deletion rates at 11 chromosomal positions and the fitness effects of several spontaneous deletions. Deletion rates varied over 200-fold between different regions with the replication terminus region showing the highest rates. Approximately 25% of the examined deletions caused an increase in fitness under one or several growth conditions, and after serial passage of wild-type bacteria in rich medium for 1,000 generations we observed fixation of deletions that substantially increased bacterial fitness when reconstructed in a non-evolved bacterium. These results suggest that selection could be a significant driver of gene loss and reductive genome evolution.

The lac repressor displays facilitated diffusion in living cells.

Transcription factors (TFs) are proteins that regulate the expression of genes by binding sequence-specific sites on the chromosome. It has been proposed that to find these sites fast and accurately, TFs combine one-dimensional (1D) sliding on DNA with 3D diffusion in the cytoplasm. This facilitated diffusion mechanism has been demonstrated in vitro, but it has not been shown experimentally to be exploited in living cells. We have developed a single-molecule assay that allows us to investigate the sliding process in living bacteria. Here we show that the lac repressor slides 45 ± 10 base pairs on chromosomal DNA and that sliding can be obstructed by other DNA-bound proteins near the operator. Furthermore, the repressor frequently (>90%) slides over its natural lacO(1) operator several times before binding. This suggests a trade-off between rapid search on nonspecific sequences and fast binding at the specific sequence.

A novel lenticular arena to quantify locomotor competence in walking fruit flies.

Drosophila melanogaster has become an important invertebrate model organism in biological and medical research, for mutational and genetic analysis, and in toxicological screening. Many screening assays have been developed that assess the flies' mortality, reproduction, development, morphology, or behavioral competence. In this study, we describe a new assay for locomotor competence. It comprises a circular walking arena with a lenticular floor and a flat cover (the slope of the floor increases gradually from the center to the edge of the arena) plus automated fly tracking and statistical analysis. This simple modification of a flat arena presents a graduated physical challenge, with which we can assess fine gradations of motor ability, since a fly's time average radial distance from the arena center is a direct indicator of its climbing ability. The time averaged distribution of flies as a function of slope, activity levels, and walking speed, yields a fine grained picture of locomotory ability and motivation levels. We demonstrate the strengths and weaknesses of this assay (compared with a conventional tap-down test) by observing flies treated with a neurotoxin (BMAA) that acts as a glutamate agonist. The assay proves well suited to detect dose effects and progression effects with higher statistical power than the traditional tap-down, but it has a higher detection limit, making it less sensitive to treatment effects.