Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers.

Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.

Self-Searching Writing of Human-Organ-Scale Three-Dimensional Topographic Scaffolds with Shape Memory by Silkworm-like Electrospun Autopilot Jet.

Bioengineered scaffolds satisfying both the physiological and anatomical considerations could potentially repair partially damaged tissues to whole organs. Although three-dimensional (3D) printing has become a popular approach in making 3D topographic scaffolds, electrospinning stands out from all other techniques for fabricating extracellular matrix mimicking fibrous scaffolds. However, its complex charge-influenced jet-field interactions and the associated random motion were hardly overcome for almost a century, thus preventing it from being a viable technique for 3D topographic scaffold construction. Herein, we constructed, for the first time, geometrically challenging 3D fibrous scaffolds using biodegradable poly(ε-caprolactone), mimicking human-organ-scale face, female breast, nipple, and vascular graft, with exceptional shape memory and free-standing features by a novel field self-searching process of autopilot polymer jet, essentially resembling the silkworm-like cocoon spinning. With a simple electrospinning setup and innovative writing strategies supported by simulation, we successfully overcame the intricate jet-field interactions while preserving high-fidelity template topographies, via excellent target recognition, with pattern features ranging from 100's µm to 10's cm. A 3D cell culture study ensured the anatomical compatibility of the so-made 3D scaffolds. Our approach brings the century-old electrospinning to the new list of viable 3D scaffold constructing techniques, which goes beyond applications in tissue engineering.

Multiplexed assessment of engineered bacterial constructs for intracellular ß-galactosidase expression by redox amplification on catechol-chitosan modified nanoporous gold.

Synthetic biology approaches for rewiring of bacterial constructs to express particular intracellular factors upon induction with the target analyte are emerging as sensing paradigms for applications in environmental and in vivo monitoring. To aid in the design and optimization of bacterial constructs for sensing analytes, there is a need for lysis-free intracellular detection modalities that monitor the signal level and kinetics of expressed factors within different modified bacteria in a multiplexed manner, without requiring cumbersome surface immobilization. Herein, an electrochemical detection system on nanoporous gold that is electrofabricated with a biomaterial redox capacitor is presented for quantifying ß-galactosidase expressed inside modified Escherichia coli constructs upon induction with dopamine. This nanostructure-mediated redox amplification approach on a microfluidic platform allows for multiplexed assessment of the expressed intracellular factors from different bacterial constructs suspended in distinct microchannels, with no need for cell lysis or immobilization. Since redox mediators present over the entire depth of the microchannel can interact with the electrode and with the E. coli construct in each channel, the platform exhibits high sensitivity and enables multiplexing. We envision its application in assessing synthetic biology-based approaches for comparing specificity, sensitivity, and signal response time upon induction with target analytes of interest.

Time-Evolved SERS Signatures of DEP-Trapped Aß and Zn2+Aß Peptides Revealed by a Sub-10 nm Electrode Nanogap.

Alzheimer's disease (AD) has become highly relevant in aging societies, yet the fundamental molecular basis for AD is still poorly understood. New tools to study the undergoing structural conformation changes of amyloid beta (Aß) peptides, the pathogenic hallmark of AD, could play a crucial role in the understanding of the underlying mechanisms of misfolding and cytotoxicity of this peptide. It has been recently reported that Zn2+ interacts with Aß and changes its aggregation pathway away from less harmful fibrillar forms to more toxic species. Here, we present a versatile platform based on a set of sub-10 nm nanogap electrodes for the manipulation and sensing of biomolecules in the physiological condition at a low copy number, where molecules are trapped via dielectrophoresis (DEP) across the nanogap, which also serves as a surface-enhanced Raman spectroscopy hotspot. In this study, we demonstrate that our electrode nanogap platform can be used to study the structural difference between Aß40 and ZnAß40 peptides at different aggregation stages in the physiologically relevant concentration and in solution phase. The Raman spectroscopic signatures of the DEP-captured neuropeptides prove the device to be attractive as a label-free bioanalytical tool.

Ultrasensitive and Low-Cost Paper-Based Graphene Oxide Nanobiosensor for Monitoring Water-Borne Bacterial Contamination.

Water-borne pathogens are mostly generated due to poor sanitation, industrial effluents, and sewage sludge, leading to a significant increase in mortality rate. To prevent this, we need a simple, user-friendly, and rapid on-site detection tool of pathogens, i.e., a biosensor. As contaminated water mainly contains (80%) coliform bacteria, of which Escherichia coli is the major species, we have developed a screen-printed paper-based, label-free biosensor for the detection of E. coli in water. A nanoarchitectured graphene oxide (GO), as a fast electron-transfer flatland, was deposited on the screen-printed graphene (G) on a hydrophobic paper, followed by the immobilization of lectin Concanavalin A (ConA) as a biorecognition element for a GGO_ConA-biosensing electrode. The electrochemical characterization of GGO_ConA shows fast electron transfer with a calculated electroactive surface area of 0.16 cm2. The biosensor performance was tested in the sludge water and beach water (real sample) as an analyte using the electrochemical impedance spectroscopy (EIS) technique. The charge-transfer resistance (Rct) of GGO_ConA increases linearly with the bacterial concentration in the range of 10-108 CFU mL-1 with an estimated limit of detection (LOD) of 10 CFU mL-1, which indicates the ultrasensitivity of our biosensor, with 100 times more sensitivity than previous studies. Our reported biosensor, being cost-effective, eco-friendly, and ultrasensitive, may serve greatly as a portable monitoring kit for checking water-borne bacterial contamination.

Novel Self-Directing Single-Polymer Jet Developing Layered-Like 3D Buckled Microfibrous Scaffolds for Tissue Engineering Applications.

Electrospinning is a promising technique for the fabrication of bioscaffolds in tissue engineering applications. Pertaining issues of multiple polymer jets and bending instabilities result in random paths which lend poor controllability over scaffolds morphology for affecting the porosity and mechanical stability. The present study alleviates these challenges by demonstrating a novel self-directing single jet taking a specifically patterned path to deposit fibers into circular and uniform scaffolds without tuning any externally controlled parameters. High-speed camera observation revealed that the charge retention and dissipation on the collected fibers caused rapid autojet switching between the two jetting modes, namely, a microcantilever-like armed jet motion and a whipping motion, which sequentially expand the area and thickness of the scaffolds, respectively, in a layered-like fashion. The physical properties showed that the self-switching dual-jet modes generated multilayered microfibrous scaffolds (MFSs) with dual morphologies and varied fiber packing density, thereby establishing the gradient porosity and mechanical strength (through buckled fibers) in the scaffolds. In vitro studies showed that as-spun scaffolds are cell-permeable hierarchical 3D microporous structures enabling lateral cell seeding into multiple layers. The cell proliferation on days 6 and 9 increased 21% and 38% correspondingly on MFSs than on nanofibrous scaffolds (NFSs) done by conventional multijets electrospinning. Remarkably, this novel and single-step process is highly reproducible and tunable for developing fibrous scaffolds for tissue engineering applications.

Gelatin-polycaprolactone-nanohydroxyapatite electrospun nanocomposite scaffold for bone tissue engineering.

Bone injuries and fractures generally take a long period to heal itself. To address this problem, bone tissue engineering (BTE) has gained significant research impetus. Among the several techniques used for scaffold fabrication, electrospinning ought to be the most promising technique for the development of the nanostructured scaffolds. The present study was carried out to fabricate an electrospun nanocomposite scaffold for BTE by using gelatin, polycaprolactone (PCL), and nanohydroxyapatite (nHAp). To prepare Gelatin-PCL-nHAp nanocomposite scaffold: Gelatin-PCL blend was electrospun and then treated with nHAp (1 wt%) for different time periods. The fabricated nanocomposite scaffold was analysed by field emission scanning electron microscopy (FESEM) to determine the fiber diameter and evaluate the fiber morphology. The Gelatin-PCL-nHAp nanocomposite scaffold-20 min exhibited the average fiber diameter of 615±269 nm and average pore size 4.7±1.04 µm, and also revealed the presence of nHAp particles over the Gelatin-PCL scaffold surface. Further, X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy and thermogravimetric (TG) analysis also indicated the deposition of nHAp over the Gelatin-PCL scaffold surface. MTT assay and DNA quantification showed good viability and significant proliferation of human osteoblasts on Gelatin-PCL-nHAp nanocomposite scaffold. Moreover, cell-scaffold constructs illustrated efficient cellular attachment and adequately spread cells, and it also depicts characteristic polygonal morphology of osteoblasts over the Gelatin-PCL-nHAp nanocomposite scaffold. Thus, the results of in-vitro analysis of electrospun nanocomposite scaffold suggest that the Gelatin-PCL-nHAp scaffold can be a potential candidate for BTE applications.

Gelatin-alginate-cerium oxide nanocomposite scaffold for bone regeneration.

Worldwide the number of bone damage/fracture, due to traumatic and accidental injuries, has been growing exponentially. Currently available treatments for bone repairing are slow, and often full functional recovery is not achieved. During slow healing process, free radicals are generated at fractured site, which causes further delay in healing process. To overcome these problems, bone tissue engineering (BTE) based approaches, i.e., polymeric scaffolds loaded with free radical scavenging capabilities, seem to be a potential alternative. Cerium oxide nanoparticles (nanoceria, NC) show very good free radical scavenging capabilities. In this study, NC was incorporated in gelatin-alginate (GA) scaffolds to obtain nanocomposite scaffolds (GA-NCs) by freeze drying. Further, the effect of varying nanoceria concentration on the physicochemical and biological properties of the nanocomposite scaffolds has been evaluated. Field emission scanning electron microscopy (FESEM) images of the scaffolds revealed presence of interconnected pores. Furthermore, incorporation of NC has increased the mechanical properties, bio-mineralization, and decreased the swelling and in-vitro weight loss of the scaffolds. Additionally, GA-NCs depicts competent cell attachment, proliferation and viability. The results for osteogenic differentiation studies (i.e. ALP activity, RunX2 and osteocalcin expression) have indicated that GA-NCs scaffolds hold potential to assist differentiation of mesenchymal stem cells (MSCs) to osteoblast. Finally, the results for free radical scavenging functionality demonstrate that GA-NCs are capable of reducing free radicals. Thus, it could be stated that NC incorporated GA nanocomposite scaffold has vital importance for applications in bone tissue-engineering in future regenerative therapies.

Frequency modulation of the Min-protein oscillator by nucleoid-associated factors in Escherichia coli.

In E. coli, the Min-protein oscillator, together with the nucleoid occlusion (NO), destabilizes the Z-ring assembly away from the midcell to ensure faithful septation. These two inhibitory pathways are thought to be working independently for division site placement. Even though the Min-protein oscillator has been displayed by synthetic minimal systems, it is unclear the interplays of Min proteins and compartment geometry are sufficient to bolster oscillation stability in vivo. By probing if NO plays a role in the Min oscillation, we study the oscillation frequency in the anucleate and nucleoid-perturbed cells. Surprisingly, we found that the oscillation periods of the Min-protein oscillators were seriously deviated in the anucleate and nucleoid-perturbed cells, but the oscillation frequency either went up in the anucleate or down in the nucleoid-perturbed cells. Intriguingly, enhanced stability and reduced frequency were observed in the cells expressing the NO factor SlmA higher than the native level. Our results reveal an unanticipated role of the nucleoid in modulating the frequency and stability of Min-protein system. SlmA is indicated to facilitate such modulations, potentially via directly interacting with the Min-protein system. A fresh perspective is suggested that frequency modulation of Min-protein oscillator is mediated via the act of nucleoid-associated factors.

Cell Migration in Microfluidic Devices: Invadosomes Formation in Confined Environments.

The last 20 years have seen the blooming of microfluidics technologies applied to biological sciences. Microfluidics provides effective tools for biological analysis, allowing the experimentalists to extend their playground to single cells and single molecules, with high throughput and resolution which were inconceivable few decades ago. In particular, microfluidic devices are profoundly changing the conventional way of studying the cell motility and cell migratory dynamics. In this chapter we will furnish a comprehensive view of the advancements made in the research domain of confinement-induced cell migration, thanks to the use of microfluidic devices. The chapter is subdivided in three parts. Each section will be addressing one of the fundamental questions that the microfluidic technology is contributing to unravel: (i) where cell migration takes place, (ii) why cells migrate and, (iii) how the cells migrate. The first introductory part is devoted to a thumbnail, and partially historical, description of microfluidics and its impact in biological sciences. Stress will be put on two aspects of the devices fabrication process, which are crucial for biological applications: materials used and coating methods. The second paragraph concerns the cell migration induced by environmental cues: chemical, leading to chemotaxis, mechanical, at the basis of mechanotaxis, and electrical, which induces electrotaxis. Each of them will be addressed separately, highlighting the fundamental role of microfluidics in providing the well-controlled experimental conditions where cell migration can be induced, investigated and ultimately understood. The third part of the chapter is entirely dedicated to how the cells move in confined environments. Invadosomes (the joint name for podosomes and invadopodia) are cell protrusion that contribute actively to cell migration or invasion. The formation of invadosomes under confinement is a research topic that only recently has caught the attention of the scientific community: microfluidic design is helping shaping the future direction of this emerging field of research.

Spectral contrast imaging method for mapping transmission surface plasmon images in metallic nanostructures.

We propose a spectral contrast method to map the transmission images of surface plasmon resonance (SPR) in metallic nanostructures. Comparing the intensities between two neighboring wavelength bands near the SPR wavelength, the signal-to-noise ratio for biosensing applications obtained using the proposed method is found to be ten times higher than that obtained by conventional intensity analysis and 1.6 times better than that obtained by peak-wavelength fitting. The dynamic range and linearity of the refractive index are comparable to the peak-wavelength shift measurement. Based on the detection method, a spectral modulation system for the optical microscope is developed, combined with a gold-capped nanowire array, to measure the biointeractions in microfluidic devices. The experimental results show that the proposed method obtained multiple detections with a detection limit of 1.04 × 10-5 refractive index units. Two types of analysis methods for SPR images are used to study the protein-antibody interactions. The region-of-interest analysis supports multiplexing detections in a compact microfluidic sensor. The effective pixel analysis eliminates low-response pixels and enhances the signal-to-noise ratios for sensitive label-free detection.

Selection of aptamers for AMACR detection from DNA libraries with different primers.

In this work, we investigated aptamer selection against alpha-methylacyl-CoA racemase (AMACR) with three DNA libraries bearing different primers. Because of increased selection diversity, aptamers with varied structural properties, such as pre-folded, induced-folding, high and low primer-dependent conformations, were discovered. From the selection results, a dimeric aptamer was constructed and capable of detecting over-expression of AMACR in prostate cancer cell lines. In summary, this study demonstrates a library-based approach to obtain aptamers with different binding properties and provides distinct aptamers for flexible design of AMACR detection.

Frequency-selective electrokinetic enrichment of biomolecules in physiological media based on electrical double-layer polarization.

Proteomic biomarkers of interest to the early diagnosis of diseases and infections are present at trace levels versus interfering species. Hence, their selective enrichment is needed within bio-assays for speeding binding kinetics with receptors and for reducing signal interferences. While DC fields can separate biomolecules based on their electrokinetic mobilities, they are unable to selectively enrich biomarkers versus interfering species, which may possess like-charges. We present the utilization of AC electrokinetics to enable frequency-selective enrichment of nanocolloidal biomolecules, based on the characteristic time constant for polarization of their electrical double-layer, since surface conduction in their ion cloud depends on colloidal size, shape and surface charge. In this manner, using DC-offset AC fields, differences in frequency dispersion for negative dielectrophoresis are balanced against electrophoresis in a nanoslit channel to enable the selective enrichment of prostate specific antigen (PSA) versus anti-mouse immunoglobulin antibodies that cause signal interferences to immunoassays. Through coupling enrichment to capture by receptors on graphene-modified surfaces, we demonstrate the elimination of false positives caused by anti-mouse immunoglobulin antibodies to the PSA immunoassay.

Crowding-facilitated macromolecular transport in attractive micropost arrays.

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

10 nm deep, sub-nanoliter fluidic nanochannels on germanium for attenuated total reflection infrared (ATR-IR) spectroscopy.

The fabrication of sub-nanoliter fluidic channels is demonstrated, with merely 10 nm depth on germanium, using conventional semiconductor device fabrication methods and a polymer assisted room-temperature sealing method. As a first application, an ultralow volume (650 pL) was studied by ATR-IR spectroscopy. A detection limit of ∼7.9 × 1010 molecules of human serum albumin (HSA) (∼0.2 mM) in D2O was achieved with highly specific ATR-IR spectroscopy.

Nanofluidic Fluorescence Microscopy (NFM) for real-time monitoring of protein binding kinetics and affinity studies.

Kinetic monitoring of protein interactions offers insights to their corresponding functions in cellular processes. Surface plasmon resonance (SPR) is the current standard tool used for label-free kinetic assays; however, costly and sophisticated setups are required, decreasing its accessibility to research laboratories. We present a cost-effective nanofluidic-based immunosensor for low-noise real-time kinetic measurement of fluorescent-labeled protein binding. With the combination of fluorescence microscopy and reversed buffer flow operation, association and dissociation kinetics can be accessed in one single experiment without extra buffer loading step, which results in a simplified operation and reduced time of analysis compared to typical microfluidic immunoassays. Kinetic constants of two representative protein-ligand binding pairs (streptavidin/biotin; IgG/anti-IgG) were quantified. The good agreement of extracted rate constants with literature values and analogous SPR measurements indicates that this approach is applicable to study protein interactions of medium- and high-affinities with a limit of detection down to 1 pM, regardless of the analyte size.

Nanoslit design for ion conductivity gradient enhanced dielectrophoresis for ultrafast biomarker enrichment in physiological media.

Selective and rapid enrichment of biomolecules is of great interest for biomarker discovery, protein crystallization, and in biosensing for speeding assay kinetics and reducing signal interferences. The current state of the art is based on DC electrokinetics, wherein localized ion depletion at the microchannel to nanochannel interface is used to enhance electric fields, and the resulting biomarker electromigration is balanced against electro-osmosis in the microchannel to cause high degrees of biomarker enrichment. However, biomarker enrichment is not selective, and the levels fall off within physiological media of high conductivity, due to a reduction in ion concentration polarization and electro-osmosis effects. Herein, we present a methodology for coupling AC electrokinetics with ion concentration polarization effects in nanoslits under DC fields, for enabling ultrafast biomarker enrichment in physiological media. Using AC fields at the critical frequency necessary for negative dielectrophoresis of the biomarker of interest, along with a critical offset DC field to create proximal ion accumulation and depletion regions along the perm-selective region inside a nanoslit, we enhance the localized field and field gradient to enable biomarker enrichment over a wide spatial extent along the nanoslit length. While enrichment under DC electrokinetics relies solely on ion depletion to enhance fields, this AC electrokinetic mechanism utilizes ion depletion as well as ion accumulation regions to enhance the field and its gradient. Hence, biomarker enrichment continues to be substantial in spite of the steady drop in nanostructure perm-selectivity within physiological media.

Morphological plasticity of bacteria-Open questions.

Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular mechanisms remain largely unknown. Physical and chemical factors causing morphological changes in bacteria have been investigated and mostly associated with potential pathways linked to the cell wall synthetic machinery. These include starvation, oxidative stresses, predation effectors, antimicrobial agents, temperature stresses, osmotic shock, and mechanical constraints. In an extreme scenario of morphological plasticity, bacteria can be induced to be shapeshifters when the cell walls are defective or deficient. They follow distinct developmental pathways and transform into assorted morphological variants, and most of them would eventually revert to typical cell morphology. It is suggested that phenotypic heterogeneity might play a functional role in the development of morphological diversity and/or plasticity within an isogenic population. Accordingly, phenotypic heterogeneity and inherited morphological plasticity are found to be survival strategies adopted by bacteria in response to environmental stresses. Here, microfluidic and nanofabrication technology is considered to provide versatile solutions to induce morphological plasticity, sort and isolate morphological variants, and perform single-cell analysis including transcriptional and epigenetic profiling. Questions such as how morphogenesis network is modulated or rewired (if epigenetic controls of cell morphogenesis apply) to induce bacterial morphological plasticity could be resolved with the aid of micro-nanofluidic platforms and optimization algorithms, such as feedback system control.

Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency.

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1.

Fabrication and characterization of novel nano-biocomposite scaffold of chitosan-gelatin-alginate-hydroxyapatite for bone tissue engineering.

A novel nano-biocomposite scaffold was fabricated in bead form by applying simple foaming method, using a combination of natural polymers-chitosan, gelatin, alginate and a bioceramic-nano-hydroxyapatite (nHAp). This approach of combining nHAp with natural polymers to fabricate the composite scaffold, can provide good mechanical strength and biological property mimicking natural bone. Environmental scanning electron microscopy (ESEM) images of the nano-biocomposite scaffold revealed the presence of interconnected pores, mostly spread over the whole surface of the scaffold. The nHAp particulates have covered the surface of the composite matrix and made the surface of the scaffold rougher. The scaffold has a porosity of 82% with a mean pore size of 112±19.0µm. Swelling and degradation studies of the scaffold showed that the scaffold possesses excellent properties of hydrophilicity and biodegradability. Short term mechanical testing of the scaffold does not reveal any rupturing after agitation under physiological conditions, which is an indicative of good mechanical stability of the scaffold. In vitro cell culture studies by seeding osteoblast cells over the composite scaffold showed good cell viability, proliferation rate, adhesion and maintenance of osteoblastic phenotype as indicated by MTT assay, ESEM of cell-scaffold construct, histological staining and gene expression studies, respectively. Thus, it could be stated that the nano-biocomposite scaffold of chitosan-gelatin-alginate-nHAp has the paramount importance for applications in bone tissue-engineering in future regenerative therapies.