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Spatio-temporal control of cellular uptake achieved by photoswitchable cell-penetrating peptides
(2015)
The selective uptake of compounds into specific cells of interest is a major objective in cell biology and drug delivery. By incorporation of a novel, thermostable azobenzene moiety we generated peptides that can be switched optically between an inactive state and an active, cell-penetrating state with excellent spatio-temporal control.
NaYF4:Yb:Er nanoparticles (UCNP) were synthesized under mild experimental conditions to obtain a pure cubic lattice. Upon annealing at different temperatures up to Tan = 700 °C phase transitions to the hexagonal phase and back to the cubic phase were induced. The UCNP materials obtained for different Tan were characterized with respect to the lattice phase using standard XRD and Raman spectroscopy as well as steady state and time resolved upconversion luminescence. The standard techniques showed that for the annealing temperature range 300 °C < Tan < 600 °C the hexagonal lattice phase was dominant. For Tan < 300 °C hardly any change in the lattice phase could be deduced, whereas for Tan > 600 °C a back transfer to the α-phase was observed. Complementarily, the luminescence upconversion properties of the annealed UCNP materials were characterized in steady state and time resolved luminescence measurements. Distinct differences in the upconversion luminescence intensity, the spectral intensity distribution and the luminescence decay kinetics were found for the cubic and hexagonal lattice phases, respectively, corroborating the results of the standard analytical techniques used. In laser power dependent measurements of the upconversion luminescence intensity it was found that the green (G1, G2) and red (R) emission of Er3+ showed different effects of Tan on the number of required photons reflecting the differences in the population routes of different energy levels involved. Furthermore, the intensity ratio of Gfull/R is highly effected by the laser power only when the β-phase is present, whereas the G1/G2 intensity ratio is only slightly effected regardless of the crystal phase. Moreover, based on different upconversion luminescence kinetics characteristics of the cubic and hexagonal phase time-resolved area normalized emission spectra (TRANES) proved to be a very sensitive tool to monitor the phase transition between cubic and hexagonal phases. Based on the TRANES analysis it was possible to resolve the lattice phase transition in more detail for 200 °C < Tan < 300 °C, which was not possible with the standard techniques.
Upconversion NaYF4:Yb:Er nanoparticles co-doped with Gd3+ and Nd3+ for thermometry on the nanoscale
(2015)
In the present work, the upconversion luminescence properties of oleic acid capped NaYF4:Gd3+:Yb3+:Er3+ upconversion nanoparticles (UCNP) with pure β crystal phase and Nd3+ ions as an additional sensitizer were studied in the temperature range of 288 K < T < 328 K. The results of this study showed that the complex interplay of different mechanisms and effects, causing the special temperature behavior of the UCNP can be developed into thermometry on the nanoscale, e.g. to be applied in biological systems on a cellular level. The performance was improved by the use of Nd3+ as an additional dopant utilizing the cascade sensitization mechanism in tri-doped UCNP.
What are the fundamental laws for the adsorption of charged polymers onto oppositely charged surfaces, for convex, planar, and concave geometries? This question is at the heart of surface coating applications, various complex formation phenomena, as well as in the context of cellular and viral biophysics. It has been a long-standing challenge in theoretical polymer physics; for realistic systems the quantitative understanding is however often achievable only by computer simulations. In this study, we present the findings of such extensive Monte-Carlo in silico experiments for polymer–surface adsorption in confined domains. We study the inverted critical adsorption of finite-length polyelectrolytes in three fundamental geometries: planar slit, cylindrical pore, and spherical cavity. The scaling relations extracted from simulations for the critical surface charge density sc—defining the adsorption–desorption transition—are in excellent agreement with our analytical calculations based on the ground-state analysis of the Edwards equation. In particular, we confirm the magnitude and scaling of sc for the concave interfaces versus the Debye screening length 1/k and the extent of confinement a for these three interfaces for small ka values. For large ka the critical adsorption condition approaches the known planar limit. The transition between the two regimes takes place when the radius of surface curvature or half of the slit thickness a is of the order of 1/k. We also rationalize how sc(k) dependence gets modified for semi-flexible versus flexible chains under external confinement. We examine the implications of the chain length for critical adsorption—the effect often hard to tackle theoretically—putting an emphasis on polymers inside attractive spherical cavities. The applications of our findings to some biological systems are discussed, for instance the adsorption of nucleic acids onto the inner surfaces of cylindrical and spherical viral capsids.
The phase behavior of an amphiphilic block copolymer based on a poly(aspartic acid) hydrophilic block and a poly(n-butyl acrylate) hydrophobic block was investigated at the air–water and air–buffer interface. The polymer forms stable monomolecular films on both subphases. At low pH, the isotherms exhibit a plateau. Compression–expansion experiments and infrared reflection absorption spectroscopy suggest that the plateau is likely due to the formation of polymer bi- or multilayers. At high pH the films remain intact upon compression and no multilayer formation is observed. Furthermore, the mineralization of calcium phosphate beneath the monolayer was studied at different pH. The pH of the subphase and thus the polymer charge strongly affects the phase behavior of the film and the mineral formation. After 4 h of mineralization at low pH, atomic force microscopy shows smooth mineral films with a low roughness. With increasing pH the mineral films become inhomogeneous and the roughness increases. Transmission electron microscopy confirms this: at low pH a few small but uniform particles form whereas particles grown at higher pH are larger and highly agglomerated. Energy-dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy confirm the formation of calcium phosphate. The levels of mineralization are higher in samples grown at high pH.
Optical properties of modified diamondoids have been studied theoretically using vibrationally resolved electronic absorption, emission and resonance Raman spectra. A time-dependent correlation function approach has been used for electronic two-state models, comprising a ground state (g) and a bright, excited state (e), the latter determined from linear-response, time-dependent density functional theory (TD-DFT). The harmonic and Condon approximations were adopted. In most cases origin shifts, frequency alteration and Duschinsky rotation in excited states were considered. For other cases where no excited state geometry optimization and normal mode analysis were possible or desired, a short-time approximation was used. The optical properties and spectra have been computed for (i) a set of recently synthesized sp2/sp3 hybrid species with C[double bond, length as m-dash]C double-bond connected saturated diamondoid subunits, (ii) functionalized (mostly by thiol or thione groups) diamondoids and (iii) urotropine and other C-substituted diamondoids. The ultimate goal is to tailor optical and electronic features of diamondoids by electronic blending, functionalization and substitution, based on a molecular-level understanding of the ongoing photophysics.
Although eye movements during reading are modulated by cognitive processing demands, they also reflect visual sampling of the input, and possibly preparation of output for speech or the inner voice. By simultaneously recording eye movements and the voice during reading aloud, we obtained an output measure that constrains the length of time spent on cognitive processing. Here we investigate the dynamics of the eye-voice span (EVS), the distance between eye and voice. We show that the EVS is regulated immediately during fixation of a word by either increasing fixation duration or programming a regressive eye movement against the reading direction. EVS size at the beginning of a fixation was positively correlated with the likelihood of regressions and refixations. Regression probability was further increased if the EVS was still large at the end of a fixation: if adjustment of fixation duration did not sufficiently reduce the EVS during a fixation, then a regression rather than a refixation followed with high probability. We further show that the EVS can help understand cognitive influences on fixation duration during reading: in mixed model analyses, the EVS was a stronger predictor of fixation durations than either word frequency or word length. The EVS modulated the influence of several other predictors on single fixation durations (SFDs). For example, word-N frequency effects were larger with a large EVS, especially when word N-1 frequency was low. Finally, a comparison of SFDs during oral and silent reading showed that reading is governed by similar principles in both reading modes, although EVS maintenance and articulatory processing also cause some differences. In summary, the EVS is regulated by adjusting fixation duration and/or by programming a regressive eye movement when the EVS gets too large. Overall, the EVS appears to be directly related to updating of the working memory buffer during reading.
Background
African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii.
Results
Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome.
Conclusions
The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO.
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.
Background
Generating percentile values is helpful for the identification of children with specific fitness characteristics (i.e., low or high fitness level) to set appropriate fitness goals (i.e., fitness/health promotion and/or long-term youth athlete development). Thus, the aim of this longitudinal study was to assess physical fitness development in healthy children aged 9–12 years and to compute sex- and age-specific percentile values.
Methods
Two-hundred and forty children (88 girls, 152 boys) participated in this study and were tested for their physical fitness. Physical fitness was assessed using the 50-m sprint test (i.e., speed), the 1-kg ball push test, the triple hop test (i.e., upper- and lower- extremity muscular power), the stand-and-reach test (i.e., flexibility), the star run test (i.e., agility), and the 9-min run test (i.e., endurance). Age- and sex-specific percentile values (i.e., P10 to P90) were generated using the Lambda, Mu, and Sigma method. Adjusted (for change in body weight, height, and baseline performance) age- and sex-differences as well as the interactions thereof were expressed by calculating effect sizes (Cohen’s d).
Results
Significant main effects of Age were detected for all physical fitness tests (d = 0.40–1.34), whereas significant main effects of Sex were found for upper-extremity muscular power (d = 0.55), flexibility (d = 0.81), agility (d = 0.44), and endurance (d = 0.32) only. Further, significant Sex by Age interactions were observed for upper-extremity muscular power (d = 0.36), flexibility (d = 0.61), and agility (d = 0.27) in favor of girls. Both, linear and curvilinear shaped curves were found for percentile values across the fitness tests. Accelerated (curvilinear) improvements were observed for upper-extremity muscular power (boys: 10–11 yrs; girls: 9–11 yrs), agility (boys: 9–10 yrs; girls: 9–11 yrs), and endurance (boys: 9–10 yrs; girls: 9–10 yrs). Tabulated percentiles for the 9-min run test indicated that running distances between 1,407–1,507 m, 1,479–1,597 m, 1,423–1,654 m, and 1,433–1,666 m in 9- to 12-year-old boys and 1,262–1,362 m, 1,329–1,434 m, 1,392–1,501 m, and 1,415–1,526 m in 9- to 12-year-old girls correspond to a “medium” fitness level (i.e., P40 to P60) in this population.
Conclusions
The observed differences in physical fitness development between boys and girls illustrate that age- and sex-specific maturational processes might have an impact on the fitness status of healthy children. Our statistical analyses revealed linear (e.g., lower-extremity muscular power) and curvilinear (e.g., agility) models of fitness improvement with age which is indicative of timed and capacity-specific fitness development pattern during childhood. Lastly, the provided age- and sex-specific percentile values can be used by coaches for talent identification and by teachers for rating/grading of children’s motor performance.
Fluid force microscopy combines the positional accuracy and force sensitivity of an atomic
force microscope (AFM) with nanofluidics via a microchanneled cantilever. However, adequate
loading and cleaning procedures for such AFM micropipettes are required for various
application situations. Here, a new frontloading procedure is described for an AFM micropipette
functioning as a force- and pressure-controlled microscale liquid dispenser. This frontloading
procedure seems especially attractive when using target substances featuring high
costs or low available amounts. Here, the AFM micropipette could be filled from the tip side
with liquid from a previously applied droplet with a volume of only a few μL using a short
low-pressure pulse. The liquid-loaded AFM micropipettes could be then applied for experiments
in air or liquid environments. AFM micropipette frontloading was evaluated with the
well-known organic fluorescent dye rhodamine 6G and the AlexaFluor647-labeled antibody
goat anti-rat IgG as an example of a larger biological compound. After micropipette usage,
specific cleaning procedures were tested. Furthermore, a storage method is described, at
which the AFM micropipettes could be stored for a few hours up to several days without drying
out or clogging of the microchannel. In summary, the rapid, versatile and cost-efficient
frontloading and cleaning procedure for the repeated usage of a single AFM micropipette is
beneficial for various application situations from specific surface modifications through to
local manipulation of living cells, and provides a simplified and faster handling for already
known experiments with fluid force microscopy.
Background
Body image distortion is highly prevalent among overweight individuals. Whilst there is evidence that body-dissatisfied women and those suffering from disordered eating show a negative attentional bias towards their own unattractive body parts and others’ attractive body parts, little is known about visual attention patterns in the area of obesity and with respect to males. Since eating disorders and obesity share common features in terms of distorted body image and body dissatisfaction, the aim of this study was to examine whether overweight men and women show a similar attentional bias.
Methods/Design
We analyzed eye movements in 30 overweight individuals (18 females) and 28 normalweight individuals (16 females) with respect to the participants’ own pictures as well as gender-
and BMI-matched control pictures (front and back view). Additionally, we assessed body image and disordered eating using validated questionnaires.
Discussion
The overweight sample rated their own body as less attractive and showed a more disturbed body image. Contrary to our assumptions, they focused significantly longer on attractive
compared to unattractive regions of both their own and the control body. For one’s own body, this was more pronounced for women. A higher weight status and more frequent body checking predicted attentional bias towards attractive body parts. We found that overweight adults exhibit an unexpected and stable pattern of selective attention, with a distinctive focus on their own attractive body regions despite higher levels of body dissatisfaction. This positive attentional bias may either be an indicator of a more pronounced pattern of attentional avoidance or a self-enhancing strategy. Further research is warranted to clarify these results.
Brownianmotion is ergodic in the Boltzmann–Khinchin sense that long time averages of physical observables such as the mean squared displacement provide the same information as the corresponding ensemble average, even at out-of-equilibrium conditions. This property is the fundamental prerequisite for single particle tracking and its analysis in simple liquids. We study analytically and by event-driven molecular dynamics simulations the dynamics of force-free cooling granular gases and reveal a violation of ergodicity in this Boltzmann–
Khinchin sense as well as distinct ageing of the system. Such granular gases comprise materials such as dilute gases of stones, sand, various types of powders, or large molecules, and their mixtures are ubiquitous in Nature and technology, in particular in Space. We treat—depending on the physical-chemical properties of the inter-particle interaction upon their pair collisions—both a constant and a velocity-dependent (viscoelastic) restitution coefficient e. Moreover we compare the granular gas dynamics with an effective single particle stochastic model based on an underdamped Langevin equation with time dependent diffusivity. We find that both models share the same behaviour of the ensemble mean squared displacement (MSD) and the velocity correlations in the limit of weak dissipation. Qualitatively, the reported non-ergodic behaviour is generic for granular gases with any realistic dependence of e on the impact velocity of particles.
The present article is among the first reports on the effects of poly(ampholyte)s and poly(betaine)s on the biomimetic formation of calcium phosphate. We have synthesized a series of di- and triblock copolymers based on a non-ionic poly(ethylene oxide) block and several charged methacrylate monomers, 2-(trimethylammonium)ethyl methacrylate chloride, 2-((3-cyanopropyl)-dimethylammonium)ethyl methacrylate chloride, 3-sulfopropyl methacrylate potassium salt, and [2-(methacryloyloxy)ethyl]dimethyl-(3-sulfopropyl)ammonium hydroxide. The resulting copolymers are either positively charged, ampholytic, or betaine block copolymers. All the polymers have very high molecular weights of over 106 g mol−1. All polymers are water-soluble and show a strong effect on the precipitation and dissolution of calcium phosphate. The strongest effects are observed with triblock copolymers based on a large poly(ethylene oxide) middle block (nominal Mn = 100 000 g mol−1). Surprisingly, the data show that there is a need for positive charges in the polymers to exert tight control over mineralization and dissolution, but that the exact position of the charge in the polymer is of minor importance for both calcium phosphate precipitation and dissolution.
We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of
purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law BTh with h o 1 due to the fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided.
The interruption of learning processes by breaks filled with diverse activities is common in everyday life. We investigated the effects of active computer gaming and passive relaxation (rest and music) breaks on working memory performance. Young adults were exposed to breaks involving (i) eyes-open resting, (ii) listening to music and (iii) playing the video game “Angry Birds” before performing the n-back working memory task. Based on linear mixed-effects modeling, we found that playing the “Angry Birds” video game during a short learning break led to a decline in task performance over the course of the task as compared to eyes-open resting and listening to music, although overall task performance was not impaired. This effect was associated with high levels of daily mind wandering and low self-reported ability to concentrate. These findings indicate that video games can negatively affect working memory performance over time when played in between learning tasks. We suggest further investigation of these effects because of their relevance to everyday activity.
The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12–12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47%, timeless: 59%, bmal1: 79%) and Macrobrachium rosenbergii (clock: 100%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.
Climate change is likely to impact the seasonality and generation processes of floods in the Nordic countries, which has direct implications for flood risk assessment, design flood estimation, and hydropower production management. Using a multi-model/multi-parameter approach to simulate daily discharge for a reference (1961–1990) and a future (2071–2099) period, we analysed the projected changes in flood seasonality and generation processes in six catchments with mixed snowmelt/rainfall regimes under the current climate in Norway. The multi-model/multi-parameter ensemble consists of (i) eight combinations of global and regional climate models, (ii) two methods for adjusting the climate model output to the catchment scale, and (iii) one conceptual hydrological model with 25 calibrated parameter sets. Results indicate that autumn/winter events become more frequent in all catchments considered, which leads to an intensification of the current autumn/winter flood regime for the coastal catchments, a reduction of the dominance of spring/summer flood regimes in a high-mountain catchment, and a possible systematic shift in the current flood regimes from spring/summer to autumn/winter in the two catchments located in northern and south-eastern Norway. The changes in flood regimes result from increasing event magnitudes or frequencies, or a combination of both during autumn and winter. Changes towards more dominant autumn/winter events correspond to an increasing relevance of rainfall as a flood generating process (FGP) which is most pronounced in those catchments with the largest shifts in flood seasonality. Here, rainfall replaces snowmelt as the dominant FGP primarily due to increasing temperature.We further analysed the ensemble components in contributing to overall uncertainty in the projected changes and found that the climate
projections and the methods for downscaling or bias correction tend to be the largest contributors. The relative role of hydrological parameter uncertainty, however, is highest for those catchments showing the largest changes in flood seasonality, which confirms the lack of robustness in hydrological model parameterization for simulations under transient hydrometeorological conditions.