Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites.

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term "memory of soil". Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea-among them ammonia-oxidizing and sulphur-related types-are due obviously to former human activities and support the concept of the "ecological memory of soil".

High-frequency Contactless Sensor for the Detection of Heparin-Induced Thrombocytopenia Antibodies via Platelet Aggregation.

Heparin-induced thrombocytopenia (HIT), a severe autoimmune disorder, occurs in patients undergoing heparin therapy. The presence of platelet-activating antibodies against platelet factor 4/Heparin in the blood confirms patients suffering from HIT. The most widely used methods for HIT diagnosis are immunoassays but the results only suit to rule out HIT as the assays provide only around 50% specificity. To confirm HIT, samples with positive results in immunoassays are retested in functional assays (>98% specificity) that track platelet-activating antibodies via platelet aggregation. However, the protocols in functional assays are either time-consuming (due to the requirement of the detection of serotonin release) or require highly trained staff for the visualization of platelets. Here, we applied a cheap and easy-to-use contactless sensor, which employs high-frequency microwaves to detect the changes in the resonant frequency caused by platelet aggregation/activation. Analysis of change in conductivity and permittivity allowed us to distinguish between HIT-like (KKO) and non-HIT-like (RTO) antibodies. KKO caused a stronger reduction of conductivity of platelet samples than RTO. Our results imply that the high-frequency contactless sensor can be a promising approach for the development of a better and easier method for the detection of HIT.

Probing size variations of molecular aggregates inside chlorosomes using single-object spectroscopy.

We theoretically investigate the possibility to use single-object spectroscopy to probe size variations of the bacteriochlorophyll aggregates inside chlorosomes. Chlorosomes are the light-harvesting organelles of green sulfur and non-sulfur bacteria. They are known to be the most efficient light-harvesting systems in nature. Key to this efficiency is the organization of bacteriochlorophyll molecules in large self-assembled aggregates that define the secondary structure inside the chlorosomes. Many studies have been reported to elucidate the morphology of these aggregates and the molecular packing inside them. It is widely believed that tubular aggregates play an important role. Because the size (radius and length) of these aggregates affects the optical and excitation energy transport properties, it is of interest to be able to probe these quantities inside chlorosomes. We show that a combination of single-chlorosome linear polarization resolved spectroscopy and single-chlorosome circular dichroism spectroscopy may be used to access the typical size of the tubular aggregates within a chlorosome and, thus, probe possible variations between individual chlorosomes that may result, for instance, from different stages in growth or different growth conditions.

Emerging Structural and Interfacial Features of Particulate Polymers at the Nanoscale.

Particulate polymers at the nanoscale are exceedingly promising for diversified functional applications ranging from biomedical and energy to sensing, labeling, and catalysis. Tailored structural features (i.e., size, shape, morphology, internal softness, interior cross-linking, etc.) determine polymer nanoparticles' impact on the cargo loading capacity and controlled/sustained release, possibility of endocytosis, degradability, and photostability. The designed interfacial features, however (i.e., stimuli-responsive surfaces, wrinkling, surface porosity, shell-layer swellability, layer-by-layer surface functionalization, surface charge, etc.), regulate nanoparticles' interfacial interactions, controlled assembly, movement and collision, and compatibility with the surroundings (e.g., solvent and biological environments). These features define nanoparticles' overall properties/functions on the basis of homogeneity, stability, interfacial tension, and minimization of the surface energy barrier. Lowering of the resultant outcomes is directly influenced by inhomogeneity in the structural and interfacial design through the structure-function relationship. Therefore, a key requirement is to produce well-defined polymer nanoparticles with controlled characteristics. Polymers are amorphous, flexible, and soft, and hence controlling their structural/interfacial features through the single-step process is a challenge. The microfluidics reaction strategy is very promising because of its wide range of advantages such as efficient reactant mixing and fast phase transfer. Overall, this feature article highlights the state-of-the-art synthetic features of polymer nanoparticles with perspectives on their advanced applications.

Unraveling intra-aggregate structural disorder using single-molecule spectroscopy.

Structural disorder within self-assembled molecular aggregates may have strong effects on their optical functionality. Such disorder, however, is hard to explore using standard ensemble measurements. In this paper, we report on the characterization of intra-aggregate structural disorder through a linewidth analysis of fluorescence excitation experiments on individual zinc-chlorin (ZnChl) nanotubular molecular aggregates. Recent experiments suggest an anomaly in the linewidths of the two absorption bands that dominate the spectra: the higher-energy bands on average show a smaller linewidth than the lower-energy bands. This anomaly is explored in this paper by analyzing and modeling the correlation of the two linewidths for each aggregate. We exploit a Frenkel exciton model to show that the experimentally observed correlation of linewidths and other statistical properties of the single-aggregate spectra can be explained from small variations of the molecular orientations within individual aggregates.

Micro-Refractometry and Local-Field Mapping with Single Molecules.

The refractive index n is one of the most important materials parameters of solids and, in recent years, has become the subject of significant interdisciplinary interest, especially in nanostructures and meta-materials. It is, in principle, a macroscopic quantity, so its meaning on a length scale of a few nanometers, i.e., well below the wavelength of light, is not clear a priori and is related to methods of its measurement on this length scale. Here we introduce a novel experimental approach for mapping the effective local value [Formula: see text] of the refractive index in solid films and the analysis of related local-field enhancement effects. The approach is based on the imaging and spectroscopy of single chromophore molecules at cryogenic temperatures. Since the fluorescence lifetime T1 of dye molecules in a transparent matrix depends on the refractive index due to the local density of the electromagnetic field (i.e., of the photon states), one can obtain the local [Formula: see text] values in the surroundings of individual chromophores simply by measuring their T1 times. Spatial mapping of the local [Formula: see text] values is accomplished by localizing the corresponding chromophores with nanometer accuracy. We demonstrate this approach for a polycrystalline n-hexadecane film doped with terrylene. Unexpectedly large fluctuations of local-field effects and effective [Formula: see text] values (the latter between 1.1 and 1.9) were found.

Single-Step In Situ Assembling Routes for the Shape Control of Polymer Nanoparticles.

Controlling shapes of polymer nanoparticles via single-step process is a challenge due to their amorphous chemical nature. Precise regulation of interfacial interactions, electrical charging and reaction dynamics during ongoing polymerization process provides an environment where uniform nucleation, growth and in situ assembling can be realized, and hence nanoparticles of complex shapes can be obtained. In this work, it is investigated how in situ assembling of the growing nanoparticles succeeds and specifically in different manners by using cationic, anionic, polyionic, and nonionic surface-active agents in a time-dependent blended form. Micelle of molecular surfactants leads the spheres, but long chained polyelectrolytes support in situ assembling of growing spheres to form the nonspherical polymer nanoparticles in order to minimize the surface energy of a system. Similarly, a nonionic polymer promotes the movement of growing species in solution and allows tunable aggregation-based growth which produces more complexed nanoparticles. Furthermore, the application of acid, base and salt solution also contribute specific effect where unexpected size and shape of nanoparticles can be obtained. Overall, the roles of limited polarizability, solvation power, mobility, ionic strength, pH, and microfluidics for the synthesis of various shape-controlled polymer nanoparticles are presented here.

Defining personal utility in genomics: A Delphi study.

BACKGROUND: Individual genome sequencing results are valued by patients in ways distinct from clinical utility. Such outcomes have been described as components of "personal utility," a concept that broadly encompasses patient-endorsed benefits, that is operationally defined as non-clinical outcomes. No empirical delineation of these outcomes has been reported. AIM: To address this gap, we administered a Delphi survey to adult participants in a National Institute of Health (NIH) clinical exome study to extract the most highly endorsed outcomes constituting personal utility. MATERIALS AND METHODS: Forty research participants responded to a Delphi survey to rate 35 items identified by a systematic literature review of personal utility. RESULTS: Two rounds of ranking resulted in 24 items that represented 14 distinct elements of personal utility. Elements most highly endorsed by participants were: increased self-knowledge, knowledge of "the condition," altruism, and anticipated coping. DISCUSSION: Our findings represent the first systematic effort to delineate elements of personal utility that may be used to anticipate participant expectation and inform genetic counseling prior to sequencing. The 24 items reported need to be studied further in additional clinical genome sequencing studies to assess generalizability in other populations. Further research will help to understand motivations and to predict the meaning and use of results.

Excited state dynamics and conformations of a Cu(ii)-phthalocyanine-perylenebisimide dyad.

We investigate the excited state dynamics and the conformations of a new molecular donor-bridge-acceptor system, a Cu(ii)-phthalocyanine (CuPc) covalently linked via a flexible aliphatic spacer to a perylenebisimide (PBI). We performed time-resolved polarization anisotropy and pump-probe measurements in combination with molecular dynamics simulations. Our data suggest the existence of three conformations of the dyad: two more extended, metastable conformations with centre-of-mass distances >1 nm between the PBI and CuPc units of the dyad, and a highly stable folded structure, in which the PBI and CuPc units are stacked on top of each other with a centre-of-mass distance of 0.4 nm. In the extended conformations the dyad shows emission predominantly from the PBI unit with a very weak contribution from the CuPc unit. In contrast, for the folded conformation the PBI emission of the dyad is strongly quenched due to fast energy transfer from the PBI to the CuPc unit (3 ps) and subsequent intersystem-crossing (300 fs) from the first excited singlet state of CuPc unit into its triplet state. Finally, the CuPc triplet state is deactivated non-radiatively with a time constant of 25 ns.

Complex Squeezing and Force Measurement Beyond the Standard Quantum Limit.

A continuous quantum field, such as a propagating beam of light, may be characterized by a squeezing spectrum that is inhomogeneous in frequency. We point out that homodyne detectors, which are commonly employed to detect quantum squeezing, are blind to squeezing spectra in which the correlation between amplitude and phase fluctuations is complex. We find theoretically that such complex squeezing is a component of ponderomotive squeezing of light through cavity optomechanics. We propose a detection scheme called synodyne detection, which reveals complex squeezing and allows the accounting of measurement backaction. Even with the optomechanical system subject to continuous measurement, such detection allows the measurement of one component of an external force with sensitivity only limited by the mechanical oscillator's thermal occupation.

Preparation and characterization of a possible topological insulator BiYO3: experiment versus theory.

The Bi-Y-O system has been investigated by X-ray powder diffraction, electron diffraction, UV-vis and IR experiments. A metastable cubic high temperature phase of BiYO3 with fluorite-type structure has been structurally characterized for the first time and shows a large band gap of ∼ 5.9 eV. A unified description for the numerous structural variants discovered in the Bi-Y-O system is established within the symmetry breaking approach. This rich structural phenomenon makes the Bi-Y-O system a promising candidate in the search for new topological insulators for applications. On this basis, a long standing controversy on the phase diagram of the Bi-Y-O system has been solved. Our DFT calculations predict a high pressure phase for BiYO3 with perovskite (ABO3) structure and ordering of Bi and Y on the A and B sites, respectively. However, our analysis of the nature of the low energy electronic structure shows that this phase is not a suitable candidate for a topological insulator.

Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition.

The recovery of species composition and functions of soil microbial community of degraded lands is crucial in order to guarantee the long-term self-sustainability of the ecosystems. A field experiment was carried out to test the influence of combining fermented sugar beet residue (SBR) addition and inoculation with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae on the plant growth parameters and microbial community composition and function in the rhizosphere of two autochthonous plant species (Dorycnium pentaphyllum L. and Asteriscus maritimus L.) growing in a semiarid soil contaminated by heavy metals. We analysed the phospholipid fatty acids (PLFAs), neutral lipids fatty acids (NLFAs) and enzyme activities to study the soil microbial community composition and function, respectively. The combined treatment was not effective for increasing plant growth. The SBR promoted the growth of both plant species, whilst the AM fungus was effective only for D. pentaphyllum. The effect of the treatments on plant growth was linked to shifts in the rhizosphere microbial community composition and function. The highest increase in dehydrogenase and ß-glucosidase activities was recorded in SBR-amended soil. The SBR increased the abundance of marker PLFAs for saprophytic fungi, Gram+ and Gram- bacteria and actinobacteria, whereas the AM fungus enhanced the abundance of AM fungi-related NLFA and marker PLFAs for Gram- bacteria. Measurement of the soil microbial community composition and function was useful to assess the success of phytomanagement technologies in a semiarid, contaminated soil.

[Current Practice of Dealing with Comorbid Problematic Substance Use in Non-Specialized Rehabilitation Settings: A Survey in German Somatic and Psychosomatic Rehabilitation Centres]. / Gegenwärtige Praxis des Umgangs mit komorbidem problematischem Suchtmittelkonsum in nicht auf Sucht spezialisierten Rehabilitationseinrichtungen--Ergebnisse einer deutschlandweiten Befragung.

STUDY OBJECTIVE: The current practice of dealing with comorbid problematic substance use in non-specialized somatic and psychosomatic rehabilitation centres is described. METHODS: A nationwide survey of rehabilitation centres across all indications was conducted. RESULTS: Incidents related to substance use within the past 12 months were reported by every centre participating in the survey. Even though these incidents occurred rather infrequently, 85% of the respondents stated that the opportunity should be used to address the topic of problematic substance use with all patients. At the same time the issue is discussed controversially by staff members in 42% of the centres, and 29% of the respondents state that there is a need to change the way this issue is dealt with. CONCLUSION: It seems necessary to strengthen the awareness of the problem as well as the professional confidence in dealing with it. In order to support identification of and dealing with problematic substance use, appropriate practice guidelines for the somatic and psychosomatic rehabilitation settings are needed. The present survey constitutes a basis for developing such practice guidelines.

Influence of segmental chromosome abnormalities on survival in children over the age of 12 months with unresectable localised peripheral neuroblastic tumours without MYCN amplification.

BACKGROUND: The prognostic impact of segmental chromosome alterations (SCAs) in children older than 1 year, diagnosed with localised unresectable neuroblastoma (NB) without MYCN amplification enrolled in the European Unresectable Neuroblastoma (EUNB) protocol is still to be clarified, while, for other group of patients, the presence of SCAs is associated with poor prognosis. METHODS: To understand the role of SCAs we performed multilocus/pangenomic analysis of 98 tumour samples from patients enrolled in the EUNB protocol. RESULTS: Age at diagnosis was categorised into two groups using 18 months as the age cutoff. Significant difference in the presence of SCAs was seen in tumours of patients between 12 and 18 months and over 18 months of age at diagnosis, respectively (P=0.04). A significant correlation (P=0.03) was observed between number of SCAs per tumour and age. Event-free (EFS) and overall survival (OS) were calculated in both age groups, according to both the presence and number of SCAs. In older patients, a poorer survival was associated with the presence of SCAs (EFS=46% vs 75%, P=0.023; OS=66.8% vs 100%, P=0.003). Moreover, OS of older patients inversely correlated with number of SCAs (P=0.002). Finally, SCAs provided additional prognostic information beyond histoprognosis, as their presence was associated with poorer OS in patients over 18 months with unfavourable International Neuroblastoma Pathology Classification (INPC) histopathology (P=0.018). CONCLUSIONS: The presence of SCAs is a negative prognostic marker that impairs outcome of patients over the age of 18 months with localised unresectable NB without MYCN amplification, especially when more than one SCA is present. Moreover, in older patients with unfavourable INPC tumour histoprognosis, the presence of SCAs significantly affects OS.

Microfluidic Assisted Synthesis of Multipurpose Polymer Nanoassembly Particles for Fluorescence, LSPR, and SERS Activities.

Potential biomedical applications such as controlled delivery with sustained drug release profile demand for multifunctional polymeric particles of precise chemical composition and with welldefined physicochemical properties. The real challenge is to obtain the reproducible and homogeneous nanoparticles in a minimum number of preparation steps. Here, single-step nanoarchitectures of soft surface layered copolymer nanoparticles with a regular tuning in the size via micro flow-through assisted synthesis are reported. Interfacial copolymerization induces the controlled compartmentalization where a hydrophobic core adopts spherical shape in order to minimize the surface energy and simultaneously shelter in the hydrophilic shelllike surface layer. Surface layer can swell in the aqueous medium and allow controlled entrapping of functional hydrophobic nanoparticles in the hydrophilic interior via electrostatic interaction which can be particularly interesting for combined fluorescence activity. Furthermore, the nanoarchitecture of size and concentration controlled polymer-metal nanoassembly particles can be implemented as an ideal surface-enhanced Raman scattering substrate for detection of the trace amounts of various analytes.

Whole-lake experiments reveal the fate of terrestrial particulate organic carbon in benthic food webs of shallow lakes.

Lake ecosystems are strongly linked to their terrestrial surroundings by material and energy fluxes across ecosystem boundaries. However, the contribution of terrestrial particulate organic carbon (tPOC) from annual leaf fall to lake food webs has not yet been adequately traced and quantified. In this study, we conducted whole-lake experiments to trace artificially added tPOC through the food webs of two shallow lakes of similar eutrophic status, but featuring alternative stable regimes (macrophyte rich vs. phytoplankton dominated). Lakes were divided with a curtain, and maize (Zea mays) leaves were added, as an isotopically distinct tPOC source, into one half of each lake. To estimate the balance between autochthonous carbon fixation and allochthonous carbon input, primary production and tPOC and tDOC (terrestrial dissolved organic carbon) influx were calculated for the treatment sides. We measured the stable isotope ratios of carbon (delta13C) of about 800 samples from all trophic consumer levels and compared them between lake sides, lakes, and three seasons. Leaf litter bag experiments showed that added maize leaves were processed at rates similar to those observed for leaves from shoreline plants, supporting the suitability of maize leaves as a tracer. The lake-wide carbon influx estimates confirmed that autochthonous carbon fixation by primary production was the dominant carbon source for consumers in the lakes. Nevertheless, carbon isotope values of benthic macroinvertebrates were significantly higher with maize additions compared to the reference side of each lake. Carbon isotope values of omnivorous and piscivorous fish were significantly affected by maize additions only in the macrophyte-dominated lake and delta13C of zooplankton and planktivorous fish remained unaffected in both lakes. In summary, our results experimentally demonstrate that tPOC in form of autumnal litterfall is rapidly processed during the subsequent months in the food web of shallow lakes and is channeled to secondary and tertiary consumers predominantly via the benthic pathways. A more intense processing of tPOC seems to be connected to a higher structural complexity in littoral zones, and hence may differ between shallow lakes of alternative stable states.

Control of shape and size of polymer nanoparticles aggregates in a single-step microcontinuous flow process: a case of flower and spherical shapes.

Controlled aggregation of polymer nanoparticles for building anisotropic nano- and microstructures via a self-assembling bottom-up process is an important strategy. Therefore, in this work, the formation of structured poly(methyl methacrylate) (PMMA) particles with diameters between lower micrometer and submicrometer range by use of a microcontinuous flow arrangement was investigated in the presence of nonionic water-soluble polymer polyvinylpyrrolidone (PVP). The investigations show that the microreaction strategy is well applicable and allows a tuning of size and shape of nanoparticles in dependence on reactant concentrations and flow rate ratios. Larger and complex structured polymer particles have been found at lower PVP concentration, whereas more compact submicron-sized particles were formed at higher PVP concentrations. The addition of ionic surfactants modulates the generation of characteristic particle shapes. The observation of intermediate states between complex flowerlike particles and simple spheres in dependence on the applied concentration of low molecular weight surfactants supports the explanation of particle formation by a mechanism with superposition of particle growth and assembling. When mixed surfactants (PVP-SDS or PVP-CTAB) are used, the final particles shape depends on the concentration of individual concentrations of surfactants and on the competition between mobility, solvation, and micelle formations.

Unravelling the conformations of di-(perylene bisimide acrylate) by combining time-resolved fluorescence-anisotropy experiments and molecular modelling.

We compare the results from time-resolved fluorescence anisotropy experiments and molecular modelling on perylene bisimide acrylate dimers which allows us to connect the observed spectral signatures unambiguously with the non-stacked and two (parallel and anti-parallel) stacked conformations. For the parallel stacked conformation the experimental data can be reproduced quantitatively using a model that assumes structural relaxation in the electronically excited state of the stacked aggregate. For the non-stacked conformation we find quantitative agreement between experiment and modelling only if a fast hopping of the electronic excitation between the perylene bisimide subunits is taken into account.

Polyacrylamid/silver composite particles produced via microfluidic photopolymerization for single particle-based SERS microsensorics.

A micro-continuous-flow process was applied for the preparation of swellable polyacrylamide particles incorporating silver nanoparticles. These sensor particles are formed from a mixture of a colloidal solution of silver nanoparticles and monomer by a droplet-based procedure with in situ photoinitiation of polymerization and a subsequent silver enforcement in batch. The obtained polymer composite particles show a strong SERS effect. Characteristic Raman signals of aqueous solutions of adenine could be detected down to 0.1 µM by the use of single sensor particles. The chosen example demonstrates that the composite particles are suitable for quantitative microanalytical procedures with a high dynamic range (3 orders of magnitude for adenine).

A self-seeding synthesis of Ag microrods of tuned aspect ratio: ascorbic acid plays a key role.

Control of the shape and size of nanoparticles is crucial for using them as labels or as building blocks in nanotechnology. In fact, silver has so far been considered as having the widest variety of different morphologies at the nano-scale and micro-scale levels. To make progress in these criteria, in our paper we have synthesized highly reproducible silver (Ag) microrods of controlled aspect ratios through a rapid self-seeding method. The Ag nano seeds are formed via the reduction of Ag ions in hot ethylene glycol by ascorbic acid, and the subsequent growth of microrods is controlled by further deposition of Ag atoms in the presence of poly(vinylpyrrolidone). Moreover, ascorbic acid is exclusively responsible for the rod morphology, as we describe here in detail. A very low concentration of ascorbic acid forms very few Ag microrods along with a majority of Ag colloidal particles, while random overgrowth on the surfaces is observed for higher concentrations. The critical reaction condition has been found in that the aspect ratio of the Ag microrods can be systematically tuned between 4 and 90. Also, the method in which ascorbic acid is added to the reaction medium plays a key role in controlling the aspect ratio of the Ag microrods. The non-monotonic dependence of the length and the diameter of the Ag microrods has been described by an empirical equation. The function can be interpreted by means of concentration-dependent competition between the adsorption of ligands and metal deposition.