Phenylacetylene-Terminated Poly(Ethylene Glycol) as Ligands for Colloidal Noble Metal Nanoparticles: a New Tool for "Grafting to" Approach.

We report a new design of polymer phenylacetylene (PA) ligands and the ligand exchange methodology for colloidal noble metal nanoparticles (NPs). PA-terminated poly(ethylene glycol) (PEG) can bind to metal NPs through acetylide (M-C≡C-R) that affords a high grafting density. The ligand-metal interaction can be switched between σ bonding and extended π backbonding by changing grafting conditions. The σ bonding of PEG-PA with NPs is strong and it can compete with other capping ligands including thiols, while the π backbonding is much weaker. The σ bonding is also demonstrated to improve the catalytic performance of Pd for ethanol oxidation and prevent surface absorption of the reaction intermediates. Those unique binding characteristics will enrich the toolbox in the control of colloidal surface chemistry and their applications using polymer ligands.

Complete genome sequence of Microbacterium paraoxydans phage Damascus.

Phage Damascus was isolated from soil in northwestern Wisconsin using Microbacterium paraoxydans as the host. The Damascus genome is 56,477 bp with 3' single-stranded overhangs and 56.5% G+C content. Damascus was assigned to cluster EL and shares 42.6%-91.7% gene content with the three other phages in this cluster.

Pressure and Composition Effects on a Common Nanoparticle Ligand-Solvent Pair.

The effect of pressure on the properties of nanoparticles is a growing area of investigation. These measurements are typically performed in a colloidal suspension; however, pressure-induced changes in the interactions between the nanoparticle surface and the solvent are often neglected. Here, we report vibrational spectroscopy of a common nanoparticle ligand, 1-dodecanethiol, and a common solvent, toluene, under pressure. We find that the pressure-induced phase change of the 1-dodecanethiol is altered by the presence of toluene and that change depends on the concentration of the free ligand in the solution. At near-equal concentrations, phase segregation is observed and the dodecanethiol crystallizes independently from the toluene. On the other hand, at unequal concentrations, concerted phase transitions are observed in the dodecanethiol and toluene, and a disordered conformation of dodecanethiol is maintained under much higher pressures. These results shed light on the pressure-induced changes in intermolecular interactions between nanoparticle ligands and solvents, which must be considered in the design of high-pressure investigations of colloidal nanoparticles.

Correlating structural changes in thermoresponsive hydrogels to the optical response of embedded plasmonic nanoparticles.

Stimuli-responsive microgels, composed of small beads with soft, deformable polymer networks swollen through a combination of synthetic control over the polymer and its interaction with water, form a versatile platform for development of multifunctional and biocompatible sensors. The interfacial structural variation of such materials at a nanometer length scale is essential to their function, but not yet fully comprehended. Here, we take advantage of the plasmonic response of a gold nanorod embedded in a thermoresponsive microgel (AuNR@PNIPMAm) to monitor structural changes in the hydrogel directly near the nanorod surface. By direct comparison of the plasmon response against measurements of the hydrogel structure from dynamic light scattering and nuclear magnetic resonance, we find that the microgel shell of batch-polymerized AuNR@PNIPMAm exhibits a heterogeneous volume phase transition reflected by different onset temperatures for changes in the hydrodyanmic radius (RH) and plasmon resonance, respectively. The new approach of contrasting plasmonic response (a measure of local surface hydrogel structure) with RH and relaxation times paves a new path to gain valuable insight for the design of plasmonic sensors based on stimuli-responsive hydrogels.

Nucleation of Dislocations in 3.9 nm Nanocrystals at High Pressure.

As circuitry approaches single nanometer length scales, it has become important to predict the stability of single nanometer-sized metals. The behavior of metals at larger scales can be predicted based on the behavior of dislocations, but it is unclear if dislocations can form and be sustained at single nanometer dimensions. Here, we report the formation of dislocations within individual 3.9 nm Au nanocrystals under nonhydrostatic pressure in a diamond anvil cell. We used a combination of x-ray diffraction, optical absorbance spectroscopy, and molecular dynamics simulation to characterize the defects that are formed, which were found to be surface-nucleated partial dislocations. These results indicate that dislocations are still active at single nanometer length scales and can lead to permanent plasticity.

Inhibitory and nutrient use phenotypes among coexisting Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil.

Bacteria and fungi are key components of virtually all natural habitats, yet the significance of fungal-bacterial inhibitory interactions for the ecological and evolutionary dynamics of specific bacterial and fungal populations in natural habitats have been overlooked. More specifically, despite the broad consensus that antibiotics play a key role in providing a fitness advantage to competing microbes, the significance of antibiotic production in mediating cross-kingdom coevolutionary interactions has received relatively little attention. Here, we characterize reciprocal inhibition among Streptomyces and Fusarium populations from prairie soil, and explore antibiotic inhibition in relation to niche overlap among sympatric and allopatric populations. We found evidence for local adaptation between Fusarium and Streptomyces populations as indicated by significantly greater inhibition among sympatric than allopatric populations. Additionally, for both taxa, there was a significant positive correlation between the strength of inhibition against the other taxon and the intensity of resource competition from that taxon among sympatric but not allopatric populations. These data suggest that coevolutionary antagonistic interactions between Fusarium and Streptomyces are driven by resource competition, and support the hypothesis that antibiotics act as weapons in mediating bacterial-fungal interactions in soil.

Complete genome sequences of Streptomyces spp. isolated from disease-suppressive soils.

BACKGROUND: Bacteria within the genus Streptomyces remain a major source of new natural product discovery and as soil inoculants in agriculture where they promote plant growth and protect from disease. Recently, Streptomyces spp. have been implicated as important members of naturally disease-suppressive soils. To shine more light on the ecology and evolution of disease-suppressive microbial communities, we have sequenced the genome of three Streptomyces strains isolated from disease-suppressive soils and compared them to previously sequenced isolates. Strains selected for sequencing had previously showed strong phenotypes in competition or signaling assays. RESULTS: Here we present the de novo sequencing of three strains of the genus Streptomyces isolated from disease-suppressive soils to produce high-quality complete genomes. Streptomyces sp. GS93-23, Streptomyces sp. 3211-3, and Streptomyces sp. S3-4 were found to have linear chromosomes of 8.24 Mb, 8.23 Mb, and greater than 7.5 Mb, respectively. In addition, two of the strains were found to have large, linear plasmids. Each strain harbors between 26 and 38 natural product biosynthetic gene clusters, on par with previously sequenced Streptomyces spp. We compared these newly sequenced genomes with those of previously sequenced organisms. We see substantial natural product biosynthetic diversity between closely related strains, with the gain/loss of episomal DNA elements being a primary driver of genome evolution. CONCLUSIONS: Long read sequencing data facilitates large contig assembly for high-GC Streptomyces genomes. While the sample number is too small for a definitive conclusion, we do not see evidence that disease suppressive soil isolates are particularly privileged in terms of numbers of biosynthetic gene clusters. The strong sequence similarity between GS93-23 and previously isolated Streptomyces lydicus suggests that species recruitment may contribute to the evolution of disease-suppressive microbial communities.

Pseudoelasticity at Large Strains in Au Nanocrystals.

Pseudoelasticity in metals is typically associated with phase transformations (e.g., shape memory alloys) but has recently been observed in sub-10 nm Ag nanocrystals that rapidly recovered their original shape after deformation to large strains. The discovery of pseudoelasticity in nanoscale metals dramatically changes the current understanding of the properties of solids at the smallest length scales, and the motion of atoms at surfaces. Yet, it remains unclear whether pseudoelasticity exists in different metals and nanocrystal sizes. The challenge of observing deformation at atomistic to nanometer length scales has prevented a clear mechanistic understanding of nanoscale pseudoelasticity, although surface diffusion and dislocation-mediated processes have been proposed. We further the understanding of pseudoelasticity in nanoscale metals by using a diamond anvil cell to compress colloidal Au nanocrystals under quasihydrostatic and nonhydrostatic pressure conditions. Nanocrystal structural changes are measured using optical spectroscopy and transmission electron microscopy and modeled using electrodynamic theory. We find that 3.9 nm Au nanocrystals exhibit pseudoelastic shape recovery after deformation to large uniaxial strains of up to 20%, which is equivalent to an ellipsoid with an aspect ratio of 2. Nanocrystal absorbance efficiency does not recover after deformation, which indicates that crystalline defects may be trapped in the nanocrystals after deformation.

Genome Sequences for Streptomyces spp. Isolated from Disease-Suppressive Soils and Long-Term Ecological Research Sites.

We report here the high-quality genome sequences of three Streptomyces spp. isolated as part of a long-term study of microbial soil ecology. Streptomyces sp. strain GS93-23 was isolated from naturally disease-suppressive soil (DSS) in Grand Rapids, MN, and Streptomyces sp. strains S3-4 and 3211-3 were isolated from experimental plots in the Cedar Creek Ecosystem Science Reserve (CCESR).

Nanoscale manipulation of membrane curvature for probing endocytosis in live cells.

Clathrin-mediated endocytosis (CME) involves nanoscale bending and inward budding of the plasma membrane, by which cells regulate both the distribution of membrane proteins and the entry of extracellular species. Extensive studies have shown that CME proteins actively modulate the plasma membrane curvature. However, the reciprocal regulation of how the plasma membrane curvature affects the activities of endocytic proteins is much less explored, despite studies suggesting that membrane curvature itself can trigger biochemical reactions. This gap in our understanding is largely due to technical challenges in precisely controlling the membrane curvature in live cells. In this work, we use patterned nanostructures to generate well-defined membrane curvatures ranging from +50 nm to -500 nm radius of curvature. We find that the positively curved membranes are CME hotspots, and that key CME proteins, clathrin and dynamin, show a strong preference towards positive membrane curvatures with a radius <200 nm. Of ten CME-related proteins we examined, all show preferences for positively curved membrane. In contrast, other membrane-associated proteins and non-CME endocytic protein caveolin1 show no such curvature preference. Therefore, nanostructured substrates constitute a novel tool for investigating curvature-dependent processes in live cells.

Precepting Medical Students in the Patient's Presence: An Educational Randomized Trial in Family Medicine Clinic.

BACKGROUND AND OBJECTIVES: Many medical student-patient encounters occur in the outpatient setting. Conference room staffing (CRS) of student presentations has been the norm in the United States in recent decades. However, this method may not be suitable for outpatient precepting, being inefficient and reducing valuable direct face time between physician and patient. Precepting in the Presence of the Patient (PIPP) has previously been found to be an effective educational model in the outpatient setting but has never been studied in family medicine clinics, nor with non-English speaking patients, nor patients from lower socioeconomic backgrounds with low literacy. METHODS: We used a randomized controlled trial of educational models comparing time spent using PIPP with CRS in two family medicine clinics. Patient, student, and physician satisfaction were also measured using a 5-point Likert scale; total encounter time and time spent precepting were also recorded. RESULTS: PIPP is strongly preferred by attending physicians while patients and students were equally satisfied with either precepting method. PIPP provides an additional 3 minutes of physician-patient face time (17.39 versus 14.08 minutes) in an encounter that is overall shortened by 2 minutes (17.39 versus 19.71 minutes). CONCLUSIONS: PIPP is an effective method for precepting medical students in family medicine clinics, even with non-English speaking patients and those with low literacy. Given the time constraints of family physicians, PIPP should be considered as a preferred, time-efficient method for training medical students that is well received by patients, students, and particularly by physicians.

Characterizing Photon Reabsorption in Quantum Dot-Polymer Composites for Use as Displacement Sensors.

The reabsorption of photoluminescence within a medium, an effect known as the inner filter effect (IFE), has been well studied in solutions, but has garnered less attention in regards to solid-state nanocomposites. Photoluminescence from a quantum dot (QD) can selectively excite larger QDs around it resulting in a net red-shift in the reemitted photon. In CdSe/CdS core/shell QD-polymer nanocomposites, we observe a large spectral red-shift of over a third of the line width of the photoluminescence of the nanocomposites over a distance of 100 µm resulting from the IFE. Unlike fluorescent dyes, which do not show a large IFE red-shift, QDs have a component of inhomogeneous broadening that originates from their size distribution and quantum confinement. By controlling the photoluminescence broadening as well as the sample dispersion and concentration, we show that the magnitude of the IFE within the nanocomposite can be tuned. We further demonstrate that this shift can be exploited in order to spectroscopically monitor the vertical displacement of a nanocomposite in a fluorescence microscope. Large energetic shifts in the measured emission with displacement can be maximized, resulting in a displacement sensor with submicrometer resolution. We further show that the composite can be easily attached to biological samples and is able to measure deformations with high temporal and spatial precision.

Dual-Functional Lipid Coating for the Nanopillar-Based Capture of Circulating Tumor Cells with High Purity and Efficiency.

Clinical studies of circulating tumor cells (CTC) have stringent demands for high capture purity and high capture efficiency. Nanostructured surfaces have been shown to significantly increase the capture efficiency yet suffer from low capture purity. Here we introduce a dual-functional lipid coating on nanostructured surfaces. The lipid coating serves both as an effective passivation layer that helps prevent nonspecific cell adhesion and as a functionalized layer for antibody-based specific cell capture. In addition, the fluidity of lipid bilayers enables antibody clustering that enhances the cell-surface interaction for efficient cell capture. As a result, the lipid-coating method helps promote both the capture efficiency and capture purity of nanostructure-based CTC capture.

Historical sediment record and levels of PCBs in sediments and mangroves of Jobos Bay, Puerto Rico.

Polychlorinated biphenyls (PCBs) were quantified in 18 surface sediment samples, 1 sediment core, and several mangrove tissue samples collected in Jobos Bay, Puerto Rico in September 2013. Total PCBs in surface sediments ranged from 0.42 to 1232ngg-1 dw. Generally, higher levels were observed near-shore close to urban and industrial areas. The levels suggest significant pollution in Jobos Bay with respect to PCBs. Two-thirds of the sites were dominated by lighter PCB congeners (tri- to penta-chlorinated PCBs) while one-third had heavy PCB congeners (hexa- to octa-chlorinated PCBs) dominant. Total PCBs in a sediment core indicated levels fluctuating according to historical usage patterns. Total PCBs were measured in mangal leaves (14-747ngg-1 dw), roots (0.26-120ngg-1 dw), and seeds (16-93ngg-1 dw), suggesting bioaccumulation from sediments. This is the first report of a historical profile of PCBs in the study area and of PCB bioaccumulation in mangroves. This article provides new and useful information on PCBs in the Caribbean area of the GRULAC region.

Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells.

The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells.

Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome.

A conceptual model emphasizing direct host-microbe interactions has dominated work on host-associated microbiomes. To understand plant-microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant-plant and microbe-microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics.

X-ray excitable luminescent polymer dots doped with an iridium(III) complex.

In this study, cyclometalated iridium(III) complex-doped polymer dots were synthesized and shown to emit luminescence upon X-ray irradiation, potentially serving as a new probe for molecular imaging during X-ray computed tomography.

Characterization of the cell-nanopillar interface by transmission electron microscopy.

Vertically aligned nanopillars can serve as excellent electrical, optical and mechanical platforms for biological studies. However, revealing the nature of the interface between the cell and the nanopillar is very challenging. In particular, a matter of debate is whether the cell membrane remains intact around the nanopillar. Here we present a detailed characterization of the cell-nanopillar interface by transmission electron microscopy. We examined cortical neurons growing on nanopillars with diameter 50-500 nm and heights 0.5-2 µm. We found that on nanopillars less than 300 nm in diameter, the cell membrane wraps around the entirety of the nanopillar without the nanopillar penetrating into the interior of the cell. On the other hand, the cell sits on top of arrays of larger, closely spaced nanopillars. We also observed that the membrane-surface gap of both cell bodies and neurites is smaller for nanopillars than for a flat substrate. These results support a tight interaction between the cell membrane and the nanopillars and previous findings of excellent sealing in electrophysiology recordings using nanopillar electrodes.

Diarylethene doped biocompatible polymer dots for fluorescence switching.

The photochromic molecule diarylethene works as a "toggle switch" for biocompatible fluorescence polymer dots and enables fluorescence switching in biological samples.