cAMP binding to closed pacemaker ion channels is non-cooperative.

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding1. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding2,3, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP5 and provide direct validation of the ligand-induced flip-state model6-9. This approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

Structure-Driven Liquid Microjunction Surface-Sampling Probe Mass Spectrometry.

The rhizosphere is the narrow region of soil surrounding the roots of plants that is influenced by root exudates, root secretions, and associated microbial communities. This region is crucial to plant growth and development and plays a critical role in nutrient uptake, disease resistance, and soil transformation. Understanding the function of exogenous compounds in the rhizosphere starts with determining the spatiotemporal distribution of these molecular components. Using liquid microjunction surface-sampling probe mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes enables in situ, nondisruptive, and nondestructive spatiotemporal measurement of exogenous compounds from plant roots. However, long imaging times (>2 h) can negatively affect plant heath and limit temporal studies. Here, we present a novel strategy to optimize the number and location of sampling sites on these microporous membrane-covered microfluidic devices. This novel, "structure-driven" sampling workflow takes into consideration the channel structure of the microfluidic device to maximize sampling from the channels and minimize acquisition time (∼4× less time in some cases while providing similar chemical image accuracy), thus reducing stress on plants during in situ LMJ-SSP-MS analysis.

The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid.

DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle-like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a three-fold decrease in the nucleoid's volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels, the nucleoid becomes spherical, and its compressibility decreases significantly. Furthermore, we find that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid. The contribution of poly ribosomes dominates at faster and soluble proteins at slower growth rates.

High spatial and energy resolution electron energy loss spectroscopy of the magnetic and electric excitations in plasmonic nanorod oligomers.

We leverage the high spatial and energy resolution of monochromated aberration-corrected scanning transmission electron microscopy to study the hybridization of cyclic assemblies of plasmonic gold nanorods. Detailed experiments and simulations elucidate the hybridization of the coupled long-axis dipole modes into collective magnetic and electric dipole plasmon resonances. We resolve the magnetic dipole mode in these closed loop oligomers with electron energy loss spectroscopy and confirm the mode assignment with its characteristic spectrum image. The energy splitting of the magnetic mode and antibonding modes increases with the number of polygon edges (n). For the n=3-6 oligomers studied, optical simulations using normal incidence and s-polarized oblique incidence show the respective electric and magnetic modes' extinction efficiencies are maximized in the n=4 arrangement.

Publisher Correction: Reply to: On the ferroelectricity of CH3NH3PbI3 perovskites.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Total internal reflection enabled wide-field coherent anti-Stokes Raman scattering microscopy.

Wide-field coherent anti-Stokes Raman scattering (CARS) microscopy offers an attractive means for the rapid and simultaneous acquisition of vibrationally resolved images across a large field of view. A major challenge in the implementation lies in how to achieve sufficiently strong excitation fields necessary to drive the third-order optical responses over the large focal region. Here, we report a new wide-field CARS microscope enabled by a total internal reflection excitation scheme using a femtosecond Ti:Sapphire oscillator to generate pump and broadband near-infrared Stokes pulses. The spectrally broad Stokes pulse, in combination with its inherent chirp, offers not only access to a wide range of Raman modes spanning ∼1000 to ∼3500cm-1 but also a straightforward means to select vibrational transitions within this range by simply varying the time delay between the pulses. The unique capabilities of this wide-field CARS microscope were validated by acquiring high-quality CARS images from the model and complex biological samples on conventional microscope coverslips.

Chemical nature of ferroelastic twin domains in CH3NH3PbI3 perovskite.

The extraordinary optoelectronic performance of hybrid organic-inorganic perovskites has resulted in extensive efforts to unravel their properties. Recently, observations of ferroic twin domains in methylammonium lead triiodide drew significant attention as a possible explanation for the current-voltage hysteretic behaviour in these materials. However, the properties of the twin domains, their local chemistry and the chemical impact on optoelectronic performance remain unclear. Here, using multimodal chemical and functional imaging methods, we unveil the mechanical origin of the twin domain contrast observed with piezoresponse force microscopy in methylammonium lead triiodide. By combining experimental results with first principles simulations we reveal an inherent coupling between ferroelastic twin domains and chemical segregation. These results reveal an interplay of ferroic properties and chemical segregation on the optoelectronic performance of hybrid organic-inorganic perovskites, and offer an exploratory path to improving functional devices.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales.

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

Photonic crystal nanobeam biosensors based on porous silicon.

Photonic crystal (PhC) nanobeams (NB) patterned on porous silicon (PSi) waveguide substrates are demonstrated for the specific, label-free detection of oligonucleotides. These photonic structures combine the large active sensing area intrinsic to PSi sensors with the high-quality (Q) factor and low-mode volume characteristic of compact resonant silicon-on-insulator (SOI) PhC NB devices. The PSi PhC NB can achieve a Q-factor near 9,000 and has an approximately 40-fold increased active sensing area for molecular attachment, compared to traditional SOI PhC NB sensors. The PSi PhC NB exhibits a resonance shift that is more than one order of magnitude larger than that of a similarly designed SOI PhC NB for the detection of small chemical molecules and 16-base peptide nucleic acids. The design and fabrication of PSi PhC NB sensors are compatible with CMOS processing, sensor arrays, and integration with lab-on-chip systems.

Identification of Critical Surface Parameters Driving Lectin-Mediated Capture of Bacteria from Solution.

Lectin-functional interfaces are useful for isolation of bacteria from solution because they are low-cost and allow nondestructive, reversible capture. This study provides a systematic investigation of physical and chemical surface parameters that influence bacteria capture over lectin-functionalized polymer interfaces and then applies these findings to construct surfaces with significantly enhanced bacteria capture. The designer block copolymer poly(glycidyl methacrylate)- block-poly(vinyldimethyl azlactone) was used as a lectin attachment layer, and lectin coupling into the polymer film through azlactone-lectin coupling reactions was first characterized. Here, experimental parameters including polymer areal chain density, lectin molecular weight, and lectin coupling buffer were systematically varied to identify parameters driving highest azlactone conversions and corresponding lectin surface densities. To introduce physical nanostructures into the attachment layer, nanopillar arrays (NPAs) of varied heights (300 and 2100 nm) were then used to provide an underlying surface template for the functional polymer layer. Capture of Escherichia coli on lectin-polymer surfaces coated over both flat and NPA surfaces was then investigated. For flat polymer interfaces, bacteria were detected on the surface after incubation at a solution concentration of 103 cfu/mL, and a corresponding detection limit of 1.7 × 103 cfu/mL was quantified. This detection limit was 1 order of magnitude lower than control lectin surfaces functionalized with standard, carbodiimide coupling chemistry. NPA surfaces containing 300 nm tall pillars further improved the detection limit to 2.1 × 102 cfu/mL, but also reduced the viability of captured cells. Finally, to investigate the impact of cell surface parameters on capture, we used Agrobacterium tumefaciens cells genetically modified to allow manipulation of exopolysaccharide adhesin production levels. Statistical analysis of surface capture levels revealed that lectin surface density was the primary factor driving capture, as opposed to exopolysaccharide adhesin expression. These findings emphasize the critical importance of the synthetic interface and the development of surfaces that combine high lectin densities with tailored physical features to drive high levels of capture. These insights will aid in design of biofunctional interfaces with physicochemical surface properties favorable for capture and isolation of bacteria cells from solutions.

Polarization- and wavelength-resolved near-field imaging of complex plasmonic modes in Archimedean nanospirals.

Asymmetric nanophotonic structures enable a wide range of opportunities in optical nanotechnology because they support efficient optical nonlinearities mediated by multiple plasmon resonances over a broad spectral range. The Archimedean nanospiral is a canonical example of a chiral plasmonic structure because it supports even-order nonlinearities that are not generally accessible in locally symmetric geometries. However, the complex spiral response makes nanoscale experimental characterization of the plasmonic near-field structure highly desirable. Here we employ high-efficiency, high-spatial-resolution cathodoluminescence imaging in a scanning transmission electron microscope to describe the spatial, spectral, and polarization response of plasmon modes in the nanospiral geometry.

ß-(1,3)-Glucan Unmasking in Some Candida albicans Mutants Correlates with Increases in Cell Wall Surface Roughness and Decreases in Cell Wall Elasticity.

Candida albicans is among the most common human fungal pathogens, causing a broad range of infections, including life-threatening systemic infections. The cell wall of C. albicans is the interface between the fungus and the innate immune system. The cell wall is composed of an outer layer enriched in mannosylated glycoproteins (mannan) and an inner layer enriched in ß-(1,3)-glucan and chitin. Detection of C. albicans by Dectin-1, a C-type signaling lectin specific for ß-(1,3)-glucan, is important for the innate immune system to recognize systemic fungal infections. Increased exposure of ß-(1,3)-glucan to the immune system occurs when the mannan layer is altered or removed in a process called unmasking. Nanoscale changes to the cell wall during unmasking were explored in live cells with atomic force microscopy (AFM). Two mutants, the cho1Δ/Δ and kre5Δ/Δ mutants, were selected as representatives that exhibit modest and strong unmasking, respectively. Comparisons of the cho1Δ/Δ and kre5Δ/Δ mutants to the wild type reveal morphological changes in their cell walls that correlate with decreases in cell wall elasticity. In addition, AFM tips functionalized with Dectin-1 revealed that the forces of binding of Dectin-1 to all of the strains were similar, but the frequency of binding was highest for the kre5Δ/Δ mutant, decreased for the cho1Δ/Δ mutant, and rare for the wild type. These data show that nanoscale changes in surface topology are correlated with increased Dectin-1 adhesion and decreased cell wall elasticity. AFM, using tips functionalized with immunologically relevant molecules, can map epitopes of the cell wall and increase our understanding of pathogen recognition by the immune system.

Flow-Through Porous Silicon Membranes for Real-Time Label-Free Biosensing.

A flow-through sensing platform based on open-ended porous silicon (PSi) microcavity membranes that are compatible with integration in on-chip sensor arrays is demonstrated. Because of the high aspect ratio of PSi nanopores, the performance of closed-ended PSi sensors is limited by infiltration challenges and slow sensor responses when detecting large molecules such as proteins and nucleic acids. In order to improve molecule transport efficiency and reduce sensor response time, open-ended PSi nanopore membranes were used in a flow-through sensing scheme, allowing analyte solutions to pass through the nanopores. The molecular binding kinetics in these PSi membranes were compared through experiments and simulation with those from closed-ended PSi films of comparable thickness in a conventional flow-over sensing scheme. The flow-through PSi membrane resulted in a 6-fold improvement in sensor response time when detecting a high molecular weight analyte (streptavidin) versus in the flow-over PSi approach. This work demonstrates the possibility of integrating multiple flow-through PSi sensor membranes within parallel microarrays for rapid and multiplexed label-free biosensing.

Toward Microfluidic Reactors for Cell-Free Protein Synthesis at the Point-of-Care.

Cell-free protein synthesis (CFPS) is a powerful technology that allows for optimization of protein production without maintenance of a living system. Integrated within micro and nanofluidic architectures, CFPS can be optimized for point-of-care use. Here, the development of a microfluidic bioreactor designed to facilitate the production of a single-dose of a therapeutic protein, in a small footprint device at the point-of-care, is described. This new design builds on the use of a long, serpentine channel bioreactor and is enhanced by integrating a nanofabricated membrane to allow exchange of materials between parallel "reactor" and "feeder" channels. This engineered membrane facilitates the exchange of metabolites, energy, and inhibitory species, and can be altered by plasma-enhanced chemical vapor deposition and atomic layer deposition to tune the exchange rate of small molecules. This allows for extended reaction times and improved yields. Further, the reaction product and higher molecular weight components of the transcription/translation machinery in the reactor channel can be retained. It has been shown that the microscale bioreactor design produces higher protein yields than conventional tube-based batch formats, and that product yields can be dramatically improved by facilitating small molecule exchange within the dual-channel bioreactor.

Slow light Mach-Zehnder interferometer as label-free biosensor with scalable sensitivity.

The design, fabrication, and characterization of a label-free Mach-Zehnder interferometer (MZI) optical biosensor that incorporates a highly dispersive one-dimensional (1D) photonic crystal in one arm are presented. The sensitivity of this slow light MZI-based sensor scales with the length of the slow light photonic crystal region. The numerically simulated sensitivity of a MZI sensor with a 16 µm long slow light region is 115,000 rad/RIU-cm, which is sevenfold higher than traditional MZI biosensors with millimeter-length sensing regions. An experimental bulk refractive index detection sensitivity of 84,000 rad/RIU-cm is realized and nucleic acid detection is also demonstrated.

Diffusive dynamics of nanoparticles in ultra-confined media.

Differential dynamic microscopy (DDM) was used to investigate the diffusive dynamics of nanoparticles of diameter 200-400 nm that were strongly confined in a periodic square array of cylindrical nanoposts. The minimum distance between posts was 1.3-5 times the diameter of the nanoparticles. The image structure functions obtained from the DDM analysis were isotropic and could be fit by a stretched exponential function. The relaxation time scaled diffusively across the range of wave vectors studied, and the corresponding scalar diffusivities decreased monotonically with increased confinement. The decrease in diffusivity could be described by models for hindered diffusion that accounted for steric restrictions and hydrodynamic interactions. The stretching exponent decreased linearly as the nanoparticles were increasingly confined by the posts. Together, these results are consistent with a picture in which strongly confined nanoparticles experience a heterogeneous spatial environment arising from hydrodynamics and volume exclusion on time scales comparable to cage escape, leading to multiple relaxation processes and Fickian but non-Gaussian diffusive dynamics.

Selected Area Manipulation of MoS2 via Focused Electron Beam-Induced Etching for Nanoscale Device Editing.

We demonstrate direct-write patterning of single and multilayer MoS2 via a focused electron beam-induced etching (FEBIE) process mediated with the XeF2 precursor. MoS2 etching is performed at various currents, areal doses, on different substrates, and characterized using scanning electron and atomic force microscopies as well as Raman and photoluminescence spectroscopies. Scanning transmission electron microscopy reveals a sub-40 nm etching resolution and the progression of point defects and lateral etching of the consequent unsaturated bonds. The results confirm that the electron beam-induced etching process is minimally invasive to the underlying material in comparison to ion beam techniques, which damage the subsurface material. Single-layer MoS2 field-effect transistors are fabricated, and device characteristics are compared for channels that are edited via the selected area etching process. The source-drain current at constant gate and source-drain voltage scale linearly with the edited channel width. Moreover, the mobility of the narrowest channel width decreases, suggesting that backscattered and secondary electrons collaterally affect the periphery of the removed area. Focused electron beam doses on single-layer transistors below the etching threshold were also explored as a means to modify/thin the channel layer. The FEBIE exposures showed demonstrative effects via the transistor transfer characteristics, photoluminescence spectroscopy, and Raman spectroscopy. While strategies to minimize backscattered and secondary electron interactions outside of the scanned regions require further investigation, here, we show that FEBIE is a viable approach for selective nanoscale editing of MoS2 devices.

Evaporation-induced buckling and fission of microscale droplet interface bilayers.

Droplet interface bilayers (DIBs) are a robust platform for studying synthetic cellular membranes; however, to date no DIBs have been produced at cellular length scales. Here, we create microscale droplet interface bilayers (µDIBs) at the interface between aqueous femtoliter-volume droplets within an oil-filled microfluidic channel. The uniquely large area-to-volume ratio of the droplets results in strong evaporation effects, causing the system to transition through three distinct regimes. First, the two adjacent droplets shrink into the shape of a single spherical droplet, where an augmented lipid bilayer partitions two hemispherical volumes. In the second regime, the combined effects of the shrinking monolayers and growing bilayer force the confined bilayer to buckle to conserve its mass. Finally, at a critical bending moment, the buckling bilayer fissions a vesicle to regulate its shape and mass. The µDIBs produced here enable evaporation-induced bilayer dynamics reminiscent of endo- and exocytosis in cells.

Spin-flop coupling and exchange bias in embedded complex oxide micromagnets.

The magnetic domains of embedded micromagnets with 2 µm×2 µm dimensions defined in epitaxial La0.7Sr0.3MnO3 (LSMO) thin films and LaFeO3/LSMO bilayers were investigated using soft x-ray magnetic microscopy. Square micromagnets aligned with their edges parallel to the easy axes of LSMO provide an ideal experimental geometry for probing the influence of interface exchange coupling on the magnetic domain patterns. The observation of unique domain patterns not reported for ferromagnetic metal microstructures, namely divergent antiferromagnetic vortex domains and "Z"-type domains, suggests the simultaneous presence of spin-flop coupling and local exchange bias in this system.