Effects of Dissolved Gases on the Amyloid Fibril Morphology.

The onset or progression of numerous neurodegenerative diseases occurs due to aggregation of proteins that ultimately form fibrils. The assembly and morphology of fibrils are susceptible to environmental factors. In this work, we used atomic force microscopy (AFM) to investigate the effects of dissolved nitrogen and oxygen molecules on the morphology of fibrils formed by a hydrophobic amyloid peptide implicated in amyotrophic lateral sclerosis, 15 repeats of glycine-alanine, on a highly oriented pyrolytic graphite substrate. We started with preformed fibril solutions that were then diluted with buffers of different gas conditions, resulting in the aggregation of the fibrils into different morphologies that were revealed by AFM after adsorption on the substrate. Straight fibrils were observed in both degassed and ambient buffers, but a stronger lateral association was seen in degassed buffers. Smaller and softer fibrils were observed in O2-supersaturated buffers, and plaque-like fibril aggregates of considerably large size were evident in N2-supersaturated buffers. In overnight incubation experiments, we observed changes in both the morphology and height of the fibril aggregates, and their evolution varied with different gas conditions. These findings indicate that the gas type and concentration affect the aggregation of amyloid fibrils and may facilitate the development of biomaterial applications and treatments for amyloid-related diseases.

Emerging Roles of Air Gases in Lipid Bilayers.

Recent studies indicate that changing the physical properties of lipid bilayers may profoundly change the function of membrane proteins. Here, the effects of dissolved nitrogen and oxygen molecules on the mechanical properties and stability of lipid bilayers are investigated using differential confocal microscopy, atomic force microscopy, and molecular dynamics simulations. All experiments evidence the presence of dissolved air gas in lipid bilayers prepared without gas control. The lipid bilayers in degassed solutions are softer and less stable than those in ambient solutions. High concentrations of nitrogen increase the bending moduli and stability of the lipid bilayers and impede phase separation in ternary lipid bilayers. The effect of oxygen is less prominent. Molecular dynamics simulations indicate that higher nitrogen affinity accounts for increased rigidity. These findings have fundamental and wide implications for phenomena related to lipid bilayers and cell membranes, including the origin of life.

Direct comparison between subnanometer hydration structures on hydrophilic and hydrophobic surfaces via three-dimensional scanning force microscopy.

Investigating interfacial water ordering on solid surfaces with different hydrophobicities is fundamentally important. Here, we prepared hydrophilic mica substrates with some areas covered by mildly hydrophobic graphene layers and studied the resulting hydration layers using three-dimensional (3D) force measurements based on frequency-modulation atomic force microscopy. Hydration layers of 0.3-0.6 nm were detected on bare graphene regions; these layers were considerably larger than the spacing measured on mica (0.2-0.3 nm). On the graphene-covered regions, we also observed the formation of special ordered structures of adsorbates over time, on which, surprisingly, no prominent hydration layers were detected. Based on these findings, we present one possible scenario to describe the formation process of the ordered interfacial structures and the enhanced oscillation period in the force profiles. This work also demonstrates the capability and significance of 3D force measurements in probing hydration behaviors on a heterogeneous substrate with a lateral resolution smaller than several nanometers.

The Glycine-Alanine Dipeptide Repeat from C9orf72 Hexanucleotide Expansions Forms Toxic Amyloids Possessing Cell-to-Cell Transmission Properties.

Hexanucleotide expansions, GGGGCC, in the non-coding regions of the C9orf72 gene were found in major frontotemporal lobar dementia and amyotrophic lateral sclerosis patients (C9FTD/ALS). In addition to possible RNA toxicity, several dipeptide repeats (DPRs) are translated through repeat-associated non-ATG-initiated translation. The DPRs, including poly(GA), poly(GR), poly(GP), poly(PR), and poly(PA), were found in the brains and spinal cords of C9FTD/ALS patients. Among the DPRs, poly(GA) is highly susceptible to form cytoplasmic inclusions, which is a characteristic of C9FTD/ALS. To elucidate DPR aggregation, we used synthetic (GA)15 DPR as a model system to examine the aggregation and structural properties in vitro. We found that (GA)15 with 15 repeats fibrillates rapidly and ultimately forms flat, ribbon-type fibrils evidenced by transmission electron microscopy and atomic force microscopy. The fibrils are capable of amyloid dye binding and contain a characteristic cross-ß sheet structure, as revealed by x-ray scattering. Furthermore, using neuroblastoma cells, we demonstrated the neurotoxicity and cell-to-cell transmission property of (GA)15 DPR. Overall, our results show the structural and toxicity properties of GA DPR to facilitate future DPR-related therapeutic development.

Xenon gas field ion source from a single-atom tip.

Focused ion beam (FIB) systems have become powerful diagnostic and modification tools for nanoscience and nanotechnology. Gas field ion sources (GFISs) built from atomic-size emitters offer the highest brightness among all ion sources and thus can improve the spatial resolution of FIB systems. Here we show that the Ir/W(111) single-atom tip (SAT) can emit high-brightness Xe+ ion beams with a high current stability. The ion emission current versus extraction voltage was analyzed from 150 K up to 309 K. The optimal emitter temperature for maximum Xe+ ion emission was ∼150 K and the reduced brightness at the Xe gas pressure of 1 × 10-4 torr is two to three orders of magnitude higher than that of a Ga liquid metal ion source, and four to five orders of magnitude higher than that of a Xe inductively coupled plasma ion source. Most surprisingly, the SAT emitter remained stable even when operated at 309 K. Even though the ion current decreased with increasing temperature, the current at room temperature (RT) could still reach over 1 pA when the gas pressure was higher than 1 × 10-3 torr, indicating the feasibility of RT-Xe-GFIS for application to FIB systems. The operation temperature of Xe-SAT-GFIS is considerably higher than the cryogenic temperature required for the helium ion microscope (HIM), which offers great technical advantages because only simple or no cooling schemes can be adopted. Thus, Xe-GFIS-FIB would be easy to implement and may become a powerful tool for nanoscale milling and secondary ion mass spectroscopy.

High-Resolution Characterization of Preferential Gas Adsorption at the Graphene-Water Interface.

The contact of water with graphene is of fundamental importance and of great interest for numerous promising applications, but how graphene interacts with water remains unclear. Here we used atomic force microscopy (AFM) to investigate hydrophilic mica substrates with some regions covered by mechanically exfoliated graphene layers in water. In water containing air gas close to the saturation concentration (within ∼40%), cap-shaped nanostructures (or interfacial nanobubbles) and ordered-stripe domains were observed on graphene-covered regions but not on pure mica regions. These structures did not appear on graphene when samples were immersed in highly degassed water, indicating that their formation was caused by the adsorption of gas dissolved in water. Thus, atomically thin graphene, even at a narrow width of 20 nm, changes the local surface chemistry of a highly hydrophilic substrate. Furthermore, surface hydrophobicity significantly affects gas adsorption, which has broad implications for diverse phenomena in water.

Self-assembly of MinE on the membrane underlies formation of the MinE ring to sustain function of the Escherichia coli Min system.

The pole-to-pole oscillation of the Min proteins in Escherichia coli results in the inhibition of aberrant polar division, thus facilitating placement of the division septum at the midcell. MinE of the Min system forms a ring-like structure that plays a critical role in triggering the oscillation cycle. However, the mechanism underlying the formation of the MinE ring remains unclear. This study demonstrates that MinE self-assembles into fibrillar structures on the supported lipid bilayer. The MinD-interacting domain of MinE shows amyloidogenic properties, providing a possible mechanism for self-assembly of MinE. Supporting the idea, mutations in residues Ile-24 and Ile-25 of the MinD-interacting domain affect fibril formation, membrane binding ability of MinE and MinD, and subcellular localization of three Min proteins. Additional mutations in residues Ile-72 and Ile-74 suggest a role of the C-terminal domain of MinE in regulating the folding propensity of the MinD-interacting domain for different molecular interactions. The study suggests a self-assembly mechanism that may underlie the ring-like structure formed by MinE-GFP observed in vivo.

Engineered droplet-forming peptide as photocontrollable phase modulator for fused in sarcoma protein.

The assembly and disassembly of biomolecular condensates are crucial for the subcellular compartmentalization of biomolecules in the control of cellular reactions. Recently, a correlation has been discovered between the phase transition of condensates and their maturation (aggregation) process in diseases. Therefore, modulating the phase of condensates to unravel the roles of condensation has become a matter of interest. Here, we create a peptide-based phase modulator, JSF1, which forms droplets in the dark and transforms into amyloid-like fibrils upon photoinitiation, as evidenced by their distinctive nanomechanical and dynamic properties. JSF1 is found to effectively enhance the condensation of purified fused in sarcoma (FUS) protein and, upon light exposure, induce its fibrilization. We also use JSF1 to modulate the biophysical states of FUS condensates in live cells and elucidate the relationship between FUS phase transition and FUS proteinopathy, thereby shedding light on the effect of protein phase transition on cellular function and malfunction.

Assembling an ion channel: ORF 3a from SARS-CoV.

Protein 3a is a 274 amino acid polytopic channel protein with three putative transmembrane domains (TMDs) encoded by severe acute respiratory syndrome corona virus (SARS-CoV). Synthetic peptides corresponding to each of its three individual transmembrane domains (TMDs) are reconstituted into artificial lipid bilayers. Only TMD2 and TMD3 induce channel activity. Reconstitution of the peptides as TMD1 + TMD3 as well as TMD2 + TMD3 in a 1 : 1 mixture induces membrane activity for both mixtures. In a 1 : 1 : 1 mixture, channel like behavior is almost restored. Expression of full length 3a and reconstitution into artificial lipid bilayers reveal a weak cation selective (PK ≈ 2 PCl ) rectifying channel. In the presence of nonphysiological concentration of Ca-ions the channel develops channel activity.

Low-voltage and high-performance buzzer-scanner based streamlined atomic force microscope system.

In this paper we present a novel scanner design in a quad-rod actuation structure, actuated by piezoelectric disk buzzers, and a new type of atomic force microscope (AFM), which uses this buzzer-scanner and a compact disk/digital-versatile-disk astigmatic optical pickup unit (OPU) for the detection of cantilever movements. Commercially available piezoelectric disk buzzers have a low capacitance and can be driven by low-voltage signal sources, such as analog outputs from a data acquisition card, without additional voltage or current amplifiers. Various scanning ranges can be realized through changing the dimensions of the actuation structure and/or the choice of disk buzzer. We constructed a buzzer-scanner and evaluated its performance. The scanner had a scanning range of 15 µm in the X and Y directions and an actuation range of 3.5 µm on the Z axis, with nonlinearity of 2.11%, 2.73%, and 2.19% for the X,Y and Z axes, respectively. The scanner had a resonance frequency of approximately 360 Hz on the X and Y axes, and 4.12 kHz on the Z axis. An OPU-AFM with this buzzer-scanner can resolve single atomic steps of a graphite substrate with a noise level of 0.06 nm. The obtained topographic images exhibit much less distortion than those obtained with an AFM using a piezoelectric tube scanner.

Torsional resonance mode atomic force microscopy in liquid with Lorentz force actuation.

In this work, we present a design based on Lorentz force induction to excite pure torsional resonances of different types of cantilevers in air as well as in water. To demonstrate the atomic force microscopy imaging capability, the phase-modulation torsional resonance mode is employed to resolve fine features of purple membranes in a buffer solution. Most importantly, force-versus-distance curves using a relatively stiff cantilever can clearly detect the characteristic oscillatory profiles of hydration layers at a water-mica interface, indicating the high force sensitivity of the torsional mode. The high resonance frequencies and high quality-factors for the torsional mode may be of great potential for high-speed and high-sensitivity imaging in aqueous environment.

Nanomechanical recognition of prognostic biomarker suPAR with DVD-ROM optical technology.

In this work the use of a high-throughput nanomechanical detection system based on a DVD-ROM optical drive and cantilever sensors is presented for the detection of urokinase plasminogen activator receptor inflammatory biomarker (uPAR). Several large scale studies have linked elevated levels of soluble uPAR (suPAR) to infectious diseases, such as HIV, and certain types of cancer. Using hundreds of cantilevers and a DVD-based platform, cantilever deflection response from antibody-antigen recognition is investigated as a function of suPAR concentration. The goal is to provide a cheap and portable detection platform which can carry valuable prognostic information. In order to optimize the cantilever response the antibody immobilization and unspecific binding are initially characterized using quartz crystal microbalance technology. Also, the choice of antibody is explored in order to generate the largest surface stress on the cantilevers, thus increasing the signal. Using optimized experimental conditions the lowest detectable suPAR concentration is currently around 5 nM. The results reveal promising research strategies for the implementation of specific biochemical assays in a portable and high-throughput microsensor-based detection platform.

Molecular layer of gaslike domains at a hydrophobic-water interface observed by frequency-modulation atomic force microscopy.

It was numerically predicted that dissolved gas particles could enrich and adsorb at hydrophobic-liquid interfaces. Here we observe nucleation and growth of bright patches of ∼0.45 nm high on the graphite surface in pure water with frequency-modulation atomic force microscopy when the dissolved gas concentration is below the saturation level. The bright patches, suspected to be caused by adsorption of nitrogen molecules at the graphite-water interface, are composed of domains of a rowlike structure with the row separation of 4.2 ± 0.3 nm. The observation of this ordered adlayer might underline the gas segregation at various water interfaces.

Reliable preparation and regeneration of well-defined single-atom tips through laser annealing.

Single-atom tips (SATs) have crucial scientific and technological applications, such as in scanning probe microscopy and charged particle beam technology. We reported a reliable method of preparing and regenerating noble metal-covered W(111) SATs through laser annealing at approximately 1000 K under ultrahigh vacuum. The field emission patterns obtained during laser heating revealed the self-assembly process of a pyramidal tip. The SATs can be regenerated through laser annealing tens of times with little change in sharpness, indicating a long lifetime. Various pyramidal SATs can be generated and regenerated using visible-light, near-infrared, mode-locked, and continuous-wave lasers at different polarizations relative to the tip axis. The generation of well-defined pyramidal SATs through laser annealing can facilitate various applications of SATs.

Low-cost, open-source XYZ nanopositioner for high-precision analytical applications.

Nanoscale positioning has numerous applications in both academia and industry. A growing number of applications require devices with long working distances and nanoscale resolutions. Friction-inertia piezoelectric positioners, which are based on the stick-slip mechanism, achieve both nanometer resolution and centimeter-scale travel. However, the requirements of complex preload mechanism, precision machining, and precise assembly increase the cost of conventional friction-inertia nanopositioners. Herein we present the design of an open-source XYZ-axis nanopositioning system. Utilizing a magnet-based stick-slip driving mechanism, the proposed XYZ nanopositioner provides several advantages, including sub-nanometer resolution, a payload capacity of up to 12 kg (horizontal), compact size, low cost, and easy assembly; furthermore, the system is adjustment-free. The performance tests validate the precision of the system in both scanning and stepping operation modes. Moreover, the resonant spectra affirm the rigidity and dynamic response of the mechanism. In addition, we demonstrate the practical applications of this nanopositioner in various measurement techniques, including scanning electron microscopy, vibrometry, and atomic force microscopy. Furthermore, we present 11 variations of the nanopositioner designs that are either compatible with ultra-high-vacuum systems and other existing systems, 3D printable, or hacking commercial linear slides.

Fabrication of CoPt ultra-sharp single atom tips.

Two kinds of new nano tips with potential to magnetic application are fabricated. One is a PtCo alloy pyramidal tip formed by surface faceting, the other is a Pt based Co tip formed by the epitaxy with a proper growth mode. Ultra high vacuum-field ion microscopy with atomic resolution is used to investigate the atomic structures of the tip apex after various sharpen treatments.

Investigating states of gas in water encapsulated between graphene layers.

Conventionally, only two states are assumed to exist in water: well-dispersed gas monomers and gas bubbles. Rarely is this paradigm explored experimentally. To close this gap, here we used transmission electron microscopy (TEM) to study degassed water, deionized water, and gas-supersaturated water encapsulated in graphene liquid cells. While neither degassed water nor deionized water yielded specific features, two major microscopic structures were evident in gas-supersaturated water: (1) polycrystalline nanoparticles formed of gas molecules and (2) a high density of tiny cells. Dark-field TEM imaging revealed that water molecules surrounding each cell form crystalline structures-a surprising discovery of a clathrate state in gas-supersaturated water that may help resolve several long-standing puzzles. Overall, this study suggests that water may form a matrix that actively interacts with gas molecules in complex and subtle ways.

Soft-contact imaging in liquid with frequency-modulation torsion resonance mode atomic force microscopy.

In this work, we demonstrate that high-resolution imaging in water with a soft contact between the tip and the sample can be achieved with frequency-modulation torsional resonance (FM-TR) mode atomic force microscopy (AFM). This mode is very sensitive to the contact of the tip with the sample surface. A sharp jump in the resonance frequency shift occurs when the tip is getting in touch with the sample. Individual atomic features on mica surfaces can be resolved with a relatively large tip. The tip applies very small normal and lateral forces on the surface. In addition, even a long and compliant AFM cantilever can achieve a high quality factor and a high resonant frequency for the torsional oscillation in water. Along with several other advantages, this mode is very suitable for future development of high-sensitivity, high-resolution, high-speed AFM for the study of dynamic biological processes in liquid.

A horizontal-type scanning near-field optical microscope with torsional mode operation toward high-resolution and non-destructive imaging of soft materials.

We design and build a horizontal-type aperture based scanning near-field optical microscope (a-SNOM) with superior mechanical stability toward high-resolution and non-destructive topographic and optical imaging. We adopt the torsional mode in AFM (atomic force microscopy) operation to achieve a better force sensitivity and a higher topographic resolution when using pyramidal a-SNOM tips. The performance and stability of the AFM are evaluated through single-walled carbon nanotube and poly(3-hexyl-thiophene) nanowire samples. An optical resolution of 93 nm is deduced from the a-SNOM imaging of a metallic grating. Finally, a-SNOM fluorescence imaging of soft lipid domains is successfully achieved without sample damage by our horizontal-type a-SNOM instrument with torsional mode AFM operation.